PUBLICATIONS

 

Martin Karplus

 

   1.  Massachusetts Alcids,

Bull. Mass. Aud. Soc. 31, 21, 119, 151 (1947),

by M. Karplus.

 

   2.  Bird Activity in the Continuous Daylight of Arctic Summer,

Ecology 33, 129-134 (1952),

by M. Karplus.

 

   3.  Charge Distribution in the Hydrogen Molecule,

J. Chem. Phys. 25, 605-606 (1956),

by M. Karplus.

 

   4.  Valence-Bond Interpretation of Electron-Coupled Proton-Proton Magnetic Interactions Measured via

Deuterium Substitution,

J. Chem. Phys. 27, 597-598 (1957),

by M. Karplus, D. H. Anderson, T. C. Farrar, and H. S. Gutowsky.

 

   5.  Quantum-Mechanical Calculation of One-Electron Properties.  I. General Formulation,

J. Chem. Phys. 29, 1240-1246 (1958),

by M. Karplus, A. Kuppermann, and L. M. Isaacson.

 

   6.  Valence-Bond Interpretation of Electron-Coupled Nuclear Spin Interactions; Application to

Methane,

J. Chem. Phys. 30, 6-10 (1959),

by M. Karplus and D. H. Anderson.

 

   7.  Contact Electron-Spin Interactions of Nuclear Magnetic Moments,

J. Chem. Phys. 30, 11-15 (1959),

by M. Karplus.

 

   8.  Interpretation of the Electron-Spin Resonance Spectrum of the Methyl Radical,

J. Chem. Phys. 30, 15-18 (1959),

by M. Karplus.

 

   9.  Nuclear Quadrupole Interactions in Alkali Halide Molecules,

J. Chem. Phys. 30, 848-849 (1959),

by T. P. Das and M. Karplus.

 

 10.  The Quantum-Mechanical Calculation of One-Electron Properties.

II. One-and Two-Center Moment Integrals,

Zeitsch. f. Naturf. 14a, 311-318 (1959),

by A. Kuppermann, M. Karplus, and L. M. Isaacson.

 

 11.  Ligand Influence Upon Radial Wave Functions,

J. Chem. Phys. 31, 394-399 (1959),

by R. L. Belford and M. Karplus.

 

 12.  A Criterion for Orbital Hybridization and Charge Distribution in Chemical Bonds,

Proc. Natl. Acad. Sci. USA 45, 1269-1273 (1959),

by M. Karplus and D. M. Grant.

 

 13.  Angular Dependence of Electron-Coupled Proton Interactions in CH2 Groups,

J. Chem. Phys. 31, 1278-1289 (1959),

by H. S. Gutowsky, M. Karplus, and D. M. Grant.

 

 14.  Weak Interactions in Molecular Quantum Mechanics,

Rev. Mod. Phys. 32, 455-460 (1960),

by M. Karplus.

 

 15.  Note on the Internal-Rotation Barrier in Ethanic Compounds,

J. Chem. Phys. 33, 316-317 (1960),

by M. Karplus.

 

 16.  Theory of Proton Coupling Constants in Unsaturated Molecules,

J. Am. Chem. Soc. 82, 4431 (1960),

by M. Karplus.

 

 17.  "Average Energy Approximation" in Spin-Coupling Calculations,

J. Chem. Phys. 33, 941-942 (1960),

by M. Karplus.

 

 18.  The Analysis of Molecular Wave Functions by Nuclear Magnetic Resonance Spectroscopy,

J. Phys. Chem. 64, 1793-1794 (1960),

by M. Karplus.

 

 19.  Proton Spin Coupling by Pi Electrons,

J. Chem. Phys. 33, 1842-1849 (1960),

by M. Karplus.

 

 20.  Theory of Localized Contributions to the Chemical Shift. Application to Fluorobenzenes,

J. Chem. Phys. 34, 1683-1692 (1961),

by M. Karplus and T. P. Das.

 

 21.  Theoretical Interpretation of Carbon-13 Hyperfine Interactions in Electron Spin Resonance Spectra,

J. Chem. Phys. 35, 1312-1323 (1961),

by M. Karplus and G. K. Fraenkel.

 

 22.  Theory of the Spin and Charge Distribution in Aromatic Ion Radicals;

Application to the Naphthalene Negative Ion,

J. Chem. Phys. 35, 1873-1883 (1961),

by J. C. Schug, T. H. Brown, and M. Karplus.

 

 23.  Magnetic Interactions in Lithium Hydride,

J. Chem. Phys. 35, 2235-2236 (1961),

by H. J. Kolker and M. Karplus.

 

 24.  Multicenter Integrals in Molecular Quantum Mechanics,

J. Chem. Phys. 36, 550-551 (1962),

I. Shavitt and M. Karplus.

 

 25.  Deuteron Quadrupole Coupling in Diatomic "Hydrides",

J. Chem. Phys. 36, 960-965 (1962),

by H. J. Kolker and M. Karplus.

 

 26.  Magnetic Properties of Hydrogen Fluoride.  I. Rotational Moment,

J. Chem. Phys. 36, 2275-2281 (1962),

by T. P. Das and M. Karplus.

 

 27.  Magnetic Properties of Hydrogen Fluoride.  II. Susceptibility,

J. Chem. Phys. 36, 2786-2792 (1962),

by R. P. Hurst, M. Karplus, and T. P. Das.

 

 28.  Comments on the Signs of Proton Coupling Constants,

J. Am. Chem. Soc. 84, 2458 (1962),

by M. Karplus.

 

 29.  Spin Resonance Spectra of Substituted Aromatic Ions; Superposition Model,

J. Chem. Phys. 37, 330-339 (1962),

by J. C. Schug, T. H. Brown, and M. Karplus.

 

 30.  Variation-Perturbation Approach to the Interaction of Radiation with Matter,

J. Chem. Phys. 37, 2723-2724 (1962),

by M. Karplus.

 

 31.  Constrained Molecular Wavefunctions: HF Molecule,

J. Chem. Phys. 38, 44-48 (1963),

by A. Mukherji and M. Karplus.

 

 32.  Multicenter Pi-Electron Integrals for the Benzene Molecule,

J. Chem. Phys. 38, 1256-1257 (1963),

by M. Karplus and I. Shavitt.

 

 33.  Magnetic Susceptibility of Diatomic Molecules,

J. Chem. Phys. 38, 1263-1275 (1963),

by H. J. Kolker and M. Karplus.

 

 34.  An Approach to the Internal Rotation Problem,

J. Chem. Phys. 38, 1547-1552 (1963),

by M. Karplus and R. G. Parr.

 

 35.  Spin Resonance Spectra of Substituted Aromatic Ions: Perturbation Model,

J. Chem. Phys. 38, 1749-1758 (1963),

by T. H. Brown, M. Karplus, and J. C. Schug.

 

 36.  Theory of Carbon NMR Chemical Shifts in Conjugated Molecules,

J. Chem. Phys. 38, 2803-2807 (1963),

by M. Karplus and J. A. Pople.

 

 37.  Ion Radicals of Methyl-Substituted Benzenes: Temperature Dependence of Spin and Charge Densities,

J. Chem. Phys. 39, 1115-1122 (1963),

by T. H. Brown and M. Karplus.

 

 38.  A Variation-Perturbation Approach to the Interaction of Radiation with Atoms and Molecules,

J. Chem. Phys. 39, 1493-1506 (1963),

by M. Karplus and H. J. Kolker.

 

 39.  Chemical Shifts in Xenon Fluorides,

J. Chem. Phys. 39, 1611-1612 (1963),

by D. Lazdins, C. W. Kern, and M. Karplus.

 

 40.  Vicinal Proton Coupling in Nuclear Magnetic Resonance,

J. Am. Chem. Soc. 85, 2870 (1963),

by M. Karplus.

 

 41.  Electric Polarizability of Some Diatomic Molecules,

J. Chem. Phys. 39, 2011-2016 (1963),

by H. J. Kolker and M. Karplus.

 

 42.  Time-Dependent Variation-Perturbation Method for Many-Electron Systems,

J. Chem. Phys. 39, 2997-3000 (1963),

by M. Karplus and H. J. Kolker.

 

 43.  Potential Energy Surface for H3,

J. Chem. Phys. 40, 1105-1115 (1964),

by R. N. Porter and M. Karplus.

 

 44.  Analysis of Charge Distributions: Hydrogen Fluoride,

J. Chem. Phys. 40, 1374-1389 (1964),

by C. W. Kern and M. Karplus.

 

 45.  Orbital Following in the Methyl Radical,

J. Chem. Phys. 40, 1593-1601 (1964),

by D. M. Schrader and M. Karplus.

 

 46.  Dynamics of Reactive Collisions: The H+H2 Exchange Reaction,

J. Chem. Phys. 40, 2033-2034 (1964),

by M. Karplus, R. N. Porter, and R. D. Sharma.

 

 47.  Shielding Anisotropies in Xenon Fluorides,

J. Chem. Phys. 40, 3738-3739 (1964),

by M. Karplus, C. W. Kern, and D. Lazdins.

 

 48.  b-Proton Hyperfine Splittings in the Vinyl Radical,

J. Chem. Phys. 41, 56-60 (1964),

by F. J. Adrian and M. Karplus.

 

 49.  Refractive Index of the Hydrogen Molecule,

J. Chem. Phys. 41, 880-883 (1964),

by M. Karplus.

 

 50.  Theory of Nuclear Magnetic Shielding in Diatomic Molecules,

J. Chem. Phys. 41, 1259-1266 (1964),

by H. J. Kolker and M. Karplus.

 

 51.  Theoretical Investigations of Reactive Collisions in Molecular Beams: K+CH3I,

J. Chem. Phys. 41, 1267-1277 (1964),

by L. M. Raff and M. Karplus.

 

 52.  Van der Waals Forces in Atoms and Molecules,

J. Chem. Phys. 41, 3955-3961 (1964),

by H. J. Kolker and M. Karplus.

 

 53.  Nuclear Quadrupole Coupling in Polyatomic Molecules,

J. Chem. Phys. 42, 1062-1071 (1965),

by C. W. Kern and M. Karplus.

 

 54.  The Inductive Effect in the Toluene Anion Radical,

J. Am. Chem. Soc. 87, 920 (1965),

by D. Lazdins and M. Karplus.

 

 55.  Nuclear Quadrupole Interactions in Alkali Halide Molecules,

J. Chem. Phys. 42, 2885-2891 (1965),

by T. P. Das and M. Karplus.

 

 56.  Gaussian-Transform Method for Molecular Integrals.  I. Formulation for Energy Integrals,

J. Chem. Phys. 43, 398-414 (1965),

by I. Shavitt and M. Karplus.

 

 57.  Gaussian-Transform Method for Molecular Integrals.  II. Evaluation of Molecular Properties,

J. Chem. Phys. 43, 415-429 (1965),

by C. W. Kern and M. Karplus.

 

 58.  Letter to the Editor of The Times: Participation in Marches Explained,

The New York Times October 31, E13 (1965),

by O. Chamberlain, S. Coleman, D. Freedman, S. Glashow, A. Goldhaber, R. Harris, M. Karplus,

J. Rasmussen, G. Serge, R. Socolow, and H. Strauss.

 

 59.  Electron Spin Resonance Studies of Deuterium Isotope Effects.  A Novel

Resonance-Integral Perturbation,

J. Am. Chem. Soc. 87, 5260 (1965),

by M. Karplus, R. G. Lawler, and G. K. Fraenkel.

 

 60.  Exchange Reactions with Activation Energy.  I. Simple Barrier Potential for (H,H2),

J. Chem. Phys. 43, 3259-3287 (1965),

by M. Karplus, R. N. Porter, and R. D. Sharma.

 

 61.  Approximations to Hartree-Fock Perturbation Theory,

J. Chem. Phys. 44, 505-514 (1966),

by P. W. Langhoff, M. Karplus, and R. P. Hurst.

 

 62.  Theoretical Investigations of Reactive Collisions in Molecular Beams: K+CH3 I and Related Systems,

J. Chem. Phys. 44, 1212-1229 (1966),

by L. M. Raff and M. Karplus.

 

 63.  Spin Delocalization in the Allyl and Ethyl Radicals,

J. Chem. Phys. 44, 1600-1611 (1966),

by D. Lazdins and M. Karplus.

 

 64.  Distortional Effects on the Ethane Internal-Rotation Barrier,

J. Chem. Phys. 44, 3033-3037 (1966),

by O. J. Sovers and M. Karplus.

 

 65.  Studies of Zero-Field Splittings in Aromatic Molecules,

J. Chem. Phys. 44, 4459-4469 (1966),

by M. Godfrey, C. W. Kern, and M. Karplus.

 

 66.  Deuteron Quadrupole Coupling Constant in CH3D,

J. Chem. Phys. 45, 1670-1673 (1966),

by T. Caves and M. Karplus.

 

 67.  Calculation of One-Electron Properties for the Formaldehyde Molecule with the LCAO MO

SCF Function of Foster and Boys,

J. Chem. Phys. 45, 2793-2798 (1966),

by W. H. Flygare, J. M. Pochan, G. I. Kerley, T. C. Caves,

M. Karplus, S. Aung, R. M. Pitzer, and S. I. Chan.

 

 68.  Energy Dependence of Cross Sections for Hot Tritium Reactions with Hydrogen and

Deuterium Molecules,

J. Chem. Phys. 45, 3871-3873 (1966),

by M. Karplus, R. N. Porter, and R. D. Sharma.

 

 69.  Quadrupole Moment of Ethane,

J. Chem. Phys. 45, 3895-3896 (1966),

by O. J. Sovers, M. Karplus, and C. W. Kern.

 

 70.  Quasiclassical Trajectory Analysis for the Reaction of Potassium Atoms with

Oriented Methyl Iodide Molecules,

J. Am. Chem. Soc. 88, 5332 (1966),

by M. Karplus and M. Godfrey.

 

 71.  Comparison of Valence-Bond and Molecular-Orbital Results for Some Ion-Radicals,

J. Chem. Phys. 46, 870-875 (1967),

by T. H. Brown and M. Karplus.

 

 72.  Spin Delocalization in Hydrocarbon Radicals,

La Structure Hyperfine MagnÈtique des Atomes et des MolÈcules 164, 271-282 (1966),

Colloques Internationaux du Centre National de la Recherche Scientifique,

by M. Karplus and D. Lazdins.

 

 73.  Deuterium Isotope Effects in the Electron Spin Resonance Spectra of Naphthalene Negative Ions,

J. Chem. Phys. 47, 2149-2165 (1967),

by R. G. Lawler, J. R. Bolton, M. Karplus, and G. K. Fraenkel.

 

 74.  Comment on the Interpretation of Hyperconjugation and Spin Delocalization in Organic Radicals,

J. Chem. Phys. 47, 3098-3100 (1967),

by J. P. Colpa, E. de Boer, D. Lazdins, and M. Karplus.

 

 75.  Vibrational vs. Translational Activation in the H2 ,H2 and H2 ,D2 Exchange Reactions,

J. Am. Chem. Soc. 89, 5064 (1967),

by K. Morokuma, L. Pedersen, and M. Karplus.

 

 76.  Bounds for van der Waals Coefficients from PadÈ Approximants,

Phys. Rev. Letters 19, 1461-1463 (1967),

by P. W. Langhoff and M. Karplus.

 

 77.  Quantum-Mechanical Study of H+H2 Reactive Scattering,

Faraday Discussions 44, 56 (1967),

by M. Karplus and K. T. Tang.

 

 78.  Structural Implications of Reaction Kinetics,

Structural Chemistry and Molecular Biology: A Volume Dedicated to Linus Pauling

by his Students, Colleagues, and Friends, A. Rich and N. Davidson, editors, 837-847

(W. H. Freeman & Co., San Francisco, 1968),

by M. Karplus.

 

 79.  Potential-Energy Surface for H3,

J. Chem. Phys. 48, 2700-2713 (1968),

by I. Shavitt, R. M. Stevens, F. L. Minn, and M. Karplus.

 

 80.  Structure of CH3 and CF3,

J. Chem. Phys. 48, 4801-4802 (1968),

by K. Morokuma, L. Pedersen, and M. Karplus.

 

 81.  PadÈ Approximant Calculation of the Nonretarded van der Waals Coefficients for Two and

Three Helium Atoms,

Phys. Rev. 171, 70-74 (1968),

by K. T. Tang and M. Karplus.

 

 82.  Magnetic Properties and Dipole Moment of CO,

J. Chem. Phys. 49, 1094-1100 (1968),

by R. M. Stevens and M. Karplus.

 

 83.  Quantum Theory of (H,H2) Scattering: Two-Body Potential and Elastic Scattering,

J. Chem. Phys. 49, 1676-1692 (1968),

by K. T. Tang and M. Karplus.

 

 84.  Methyl Group Inductive Effect in the Toluene Ions. Comparison of H¸ckel and Extended

H¸ckel Theory,

J. Am. Chem. Soc. 90, 6275-6281 (1968),

by D. Purins and M. Karplus.

 

 85.  Theoretical Investigation of Reactive Collisions in Molecular Beams: K+Br2,

J. Chem. Phys. 49, 3602-3609 (1968),

by M. Godfrey and M. Karplus.

 

 86.  Bond-Function Analysis of Rotational Barriers: Ethane,

J. Chem. Phys. 49, 2592-2599 (1968),

by O. J. Sovers, C. W. Kern, R. M. Pitzer, and M. Karplus.

 

 87.  Symmetric H3: A Semiempirical and Ab Initio Study of a Simple Jahn-Teller System,

J. Chem. Phys. 49, 5163-5178 (1968),

by R. N. Porter, R. M. Stevens, and M. Karplus.

 

 88.  Multistructure Valence-Bond and Atoms-in-Molecules Calculations for LiF, F2, and F2-,

J. Chem. Phys. 50, 478-488 (1969),

by G. G. Balint-Kurti and M. Karplus.

 

 89.  Valence-Bond Bond-Order Formulation for Contact Nuclear Spin-Spin Coupling,

J. Am. Chem. Soc. 91, 1-10 (1969),

by M. Barfield and M. Karplus.

 

 90.  Spin Delocalization and Vibrational-Electronic Interaction in the Toluene Ion-Radicals,

J. Chem. Phys. 50, 214-233 (1969),

by D. Purins and M. Karplus.

 

 91.  Solvable Quantum-Mechanical Model of Three-Body Rearrangement Scattering,

J. Chem. Phys. 50, 1119-1126 (1969),

by K. T. Tang, B. Kleinman, and M. Karplus.

 

 92.  Proton Spin Coupling by Pi Electrons: Correction and Comments,

J. Chem. Phys. 50, 3133 (1969),

by M. Karplus.

 

 93.  Perturbed Hartree-Fock Theory. I. Diagrammatic Double-Perturbation Analysis,

J. Chem. Phys. 50, 3649-3661 (1969),

by T. C. Caves and M. Karplus.

 

 94.  PadÈ Summation of the Cauchy Dispersion Equation,

J. Opt. Soc. Am. 59, 863-871 (1969),

by P. W. Langhoff and M. Karplus.

 

 95.  Upper Bounds on Many-Channel Scattering Phase Shifts by an Adiabatic-Type Approximation,

J. Chem. Phys. 51, 2726-2734 (1969),

by R. B. Gerber and M. Karplus.

 

 96.  Collision Dynamics and the Statistical Theories of Chemical Reactions.

I. Average Cross Section from Transition-State Theory,

J. Chem. Phys. 51, 5193-5203 (1969),

by K. Morokuma, B. C. Eu, and M. Karplus.

 

 97.  Asymptotic Expansion Method for Franck-Condon Factors of Morse Oscillators,

J. Chem. Phys. 52, 783-785 (1970),

by T. Y. Chang and M. Karplus.

 

 98.  PadÈ Approximants to the Normal Dispersion Expansion of Dynamic Polarizabilities,

J. Chem. Phys. 52, 1435-1449 (1970),

by P. W. Langhoff and M. Karplus.

 

 99.  Nonequilibrium Contributions to the Rate of Reaction. I. Perturbation of the

Velocity Distribution Function,

J. Chem. Phys. 52, 4262-4278 (1970),

by B. Shizgal and M. Karplus.

 

100.  Potential-Energy Surfaces,

Rendiconti della Scuola Internazionale di Fisica "E. Fermi," XLIV Corso,

C. Schlier, editor, 320-348 (Academic Press, New York, 1970),

by M. Karplus.

 

101.  Special Results of Trajectory Studies,

Rendiconti della Scuola Internazionale di Fisica "E. Fermi," XLIV Corso,

C. Schlier, editor, 372-391 (Academic Press, New York, 1970),

by M. Karplus.

 

102.  Special Results of Theory: Distorted Waves,

Rendiconti della Scuola Internazionale di Fisica "E. Fermi," XLIV Corso,

C. Schlier, editor, 407-426 (Academic Press, New York, 1970),

by M. Karplus.

 

103.  Determination of the Phase of the Scattering Amplitude from the Differential Cross Section,

Phys. Rev. D1, 998-1012 (1970),

by R. B. Gerber and M. Karplus.

 

104.  Relativistic Long-Range Interactions between Atoms and Molecules,

J. Chem. Phys. 52, 4698-4700 (1970),

by T. Y. Chang and M. Karplus.

 

105.  PadÈ Approximants for Two- and Three-Body Dipole Dispersion Interactions,

J. Chem. Phys. 53, 233-250 (1970),

by P. W. Langhoff and M. Karplus.

 

106.  Retarded van der Waals Interactions. I. Simple Atoms,

J. Chem. Phys. 53, 2100-2106 (1970),

by P. M. Getzin and M. Karplus.

 

107.  Application of PadÈ Approximants to Dispersion Force and Optical Polarizability Computations,

The PadÈ Approximant in Theoretical Physics,

G. A. Baker and J. L. Gammel, editors, 41-97 (Academic Press, New York, 1970),

by P. W. Langhoff and M. Karplus.

 

108.  Approximate Self-Consistent-Field Study of the (NiF6)4- Cluster,

Phys. Rev. B3, 24-30 (1971),

by B. Kleinman and M. Karplus.

 

109.  Electronic Structure of Cyanide Complexes of Hemes and Heme Protein,

J. Mol. Biol. 57, 93-115 (1971),

by R. G. Shulman, S. H. Glarum, and M. Karplus.

 

110.  Differential Cross Sections for D+H2: A Comparison with Experiment,

J. Chem. Phys. 54, 5955-5957 (1971),

by P. Brumer and M. Karplus.

 

111.  Nonequilibrium Contributions to the Rate of Reactions. II. Isolated Multicomponent Systems,

J. Chem. Phys. 54, 4345-4356 (1971),

by B. Shizgal and M. Karplus.

 

112.  Nonequilibrium Contribution to the Rate of Reaction. III. Isothermal Multicomponent Systems,

J. Chem. Phys. 54, 4357-4362 (1971),

by B. Shizgal and M. Karplus.

 

113.  Ring Orientation in b-Ionone and Retinals,

Proc. Natl. Acad. Sci. USA 68, 1289-1293 (1971),

by B. Honig, B. Hudson, B. D. Sykes, and M. Karplus.

 

114.  Implications of Torsional Potential of Retinal Isomers for Visual Excitation,

Nature 229, 558-560 (1971),

by B. Honig and M. Karplus.

 

115.  Collision Dynamics and the Statistical Theories of Chemical Reactions.

II. Comparison of Reaction Probabilities,

J. Chem. Phys. 55, 63-75 (1971),

by K. Morokuma and M. Karplus.

 

116.  Comparisons of Dispersion Force Bounding Methods with Applications to Anisotropic Interactions,

J. Chem. Phys. 55, 2126-2145 (1971),

by P. W. Langhoff, R. G. Gordon, and M. Karplus.

 

117.  Potential Energy Surfaces for Simple Chemical Reactions: Li+F2 Æ LiF+F,

Chem. Phys. Letters 11, 203-207 (1971),

by G. G. Balint-Kurti and M. Karplus.

 

118.  Comparison of 3D Classical Trajectory and Transition-State Theory Reaction Cross Sections,

J. Chem. Phys. 55, 4667-4668 (1971),

by G. W. Koeppl and M. Karplus.

 

119.  Quantum Theory of (H,H2) Scattering: Approximate Treatments of Reactive Scattering,

Phys. Rev. A4, 1844-1858 (1971),

by K. T. Tang and M. Karplus.

 

120.  The Self-Consistent Random Phase Approximation,

Chem. Phys. Letters 11, 450-453 (1971),

by N. Ostlund and M. Karplus.

 

121.  Comparison of Accurate Quantum-Mechanical Probabilities with Classical and Transition-State

Theory Results for the Collinear Exchange Reaction H+H2 Æ H2 +H,

J. Chem. Phys. 55, 5832-5833 (1971),

by D. J. Diestler and M. Karplus.

 

122.  A Mathematical Model for Structure-Function Relationships in Hemoglobin,

Biochem. Biophys. Res. Commun. 46, 855 (1972),

by A. Szabo and M. Karplus.

 

123.  On the Determination of the Phases of Electromagnetic Scattering Amplitudes from Experimental Data,

J. Chem. Phys. 56, 1921-1936 (1972),

by R. B. Gerber and M. Karplus.

 

124.  Theoretical Studies of H+H2 Rotationally Inelastic Scattering,

J. Chem. Phys. 56, 4930-4946 (1972),

by G. Wolken, Jr., W. H. Miller, and M. Karplus.

 

125.  A Test of the Closed-Shell Overlap-Repulsion Model for the Ethane Barrier,

J. Am. Chem. Soc. 94, 5140 (1972),

by R. M. Stevens and M. Karplus.

 

126.  On the Origin of a Low-Lying Forbidden Transition in Polyenes and Related Molecules,

Chem. Phys. Letters 14, 305-309 (1972),

by K. Schulten and M. Karplus.

 

127.  Aspects of Time-Dependent Perturbation Theory,

Rev. Mod. Phys. 44, 602-644 (1972),

by P. W. Langhoff, S. T. Epstein, and M. Karplus.

 

128.  Calculation of Ground and Excited State Potential Surfaces of Conjugated Molecules.

I. Formulation and Parametrization,

J. Am. Chem. Soc. 94, 5612-5625 (1972),

by A. Warshel and M. Karplus.

 

129.  The Frequency-Dependent Polarizability of Hydrogen-Like Atoms,

Mol. Phys. 24, 349-355 (1972),

by P. M. Getzin and M. Karplus.

 

130.  Nuclear Magnetic Resonance Determination of the Angle j in Peptides,

Proc. Natl. Acad. Sci. USA 69, 3204-3206 (1972),

by S. Karplus and M. Karplus.

 

131.  Vibrational Structure of Electronic Transitions in Conjugated Molecules,

Chem. Phys. Letters 17, 7-14 (1972),

by A. Warshel and M. Karplus.

 

132.  A Mathematical Model for Structure-Function Relations in Hemoglobin,

J. Mol. Biol. 72, 163-197 (1972),

by A. Szabo and M. Karplus.

 

133.  Trajectory Analysis of Transition States, in Reaction Transition States,

J. E. DuBois, editor, 279-288 (Gordon & Breach, Paris, 1972),

by M. Karplus.

 

134.  The Water Molecule, inWater, A Comprehensive Treatise, I,

F. Franks, editor, 21-94 (Plenum Publishing Corp., New York, 1972),

by C. W. Kern and M. Karplus.

 

135.  Interpretation of the Binding of Carbon Monoxide to Hemoglobin Under

Photodissociating Conditions,

Proc. Natl. Acad. Sci. USA 70, 673-674 (1973),

by A. Szabo and M. Karplus.

 

136.  Perturbation Theory and Ionic Models for Alkali Halide Systems. I. Diatomics,

J. Chem. Phys. 58, 3903-3918 (1973),

by P. Brumer and M. Karplus.

 

137.  Convergence of Valence Bond and Molecular Orbital Theories,

Mol. Phys. 25, 921-936 (1973),

by W. J. Campion and M. Karplus.

 

138.  Collision Complex Dynamics in Alkali Halide Exchange Reactions,

Faraday Discussions 55, 80-91 (1973),

by P. Brumer and M. Karplus.

 

139.  Dynamics of Organic Reactions,

J. Am. Chem. Soc. 95, 8160-8164 (1973),

by I.S.Y. Wang and M. Karplus.

 

140.  Structure and Function of Hemoglobin, Proc. Rbt. A. Welch Foundation

Conference on Chem. Res. XVI. Theoretical Chemistry, 121-158 (1973),

by M. Karplus.

 

141.  Theoretical Studies of H+H2 Reactive Scattering,

J. Chem. Phys. 60, 351-367 (1974),

by G. Wolken, Jr. and M. Karplus.

 

142.  Conformation of Retinal Isomers,

Biochemistry 13, 970-981 (1974),

by R. Rowan III, A. Warshel, B. D. Sykes, and M. Karplus.

 

143.  Quantum Mechanics of Simple Chemical Reactions,

The World of Quantum Chemistry,

R. Daudel and B. Pullman, editors, 101-111 (D. Reidel Pub. Co., Dordrecht-Holland, 1974),

by M. Karplus.

 

144.  Atoms-in-Molecules, in

Orbital Theories of Molecules and Solids,

N. H. March, editor, 250-310 (Clarendon Press, Oxford, 1974),

by G. G. Balint-Kurti and M. Karplus.

 

145.  Calculation of pp* Excited State Conformations and Vibronic Structure of Retinal and

Related Molecules,

J. Am. Chem. Soc. 96, 5677-5689 (1974),

by A. Warshel and M. Karplus.

 

146.  Isotope Effect on the Hyperfine Splittings of the Deuteriobenzene Anions: An Example

of the Dynamic Jahn-Teller Effect,

J. Chem. Phys. 62, 320-332 (1975),

by D. Purins and M. Karplus.

 

147.  Analysis of Cooperativity in Hemoglobin. Valency Hybrids, Oxidations, and Methemoglobin

Replacement Reactions,

Biochemistry 14, 931-940 (1975),

by A. Szabo and M. Karplus.

 

148.  Theoretical Studies of the Visual Chromophore,

Acc. Chem. Res. 8, 92-100 (1975),

by B. Honig, A. Warshel, and M. Karplus.

 

149.  Valence-Bond Approach to Conservation of Symmetry in Concerted Reactions,

J. Am. Chem. Soc. 97, 2645-2654 (1975),

by D. M. Silver and M. Karplus.

 

150.  Sidechain Torsional Potentials and Motion of Amino Acids in Proteins:

Bovine Pancreatic Trypsin Inhibitor,

Proc. Natl. Acad. Sci. USA 72, 2002-2006 (1975),

by B. R. Gelin and M. Karplus.

 

151.  Possible Influence of a Low-Lying "Covalent" Excited State on the

Absorption Spectrum and Photoisomerization of 11-Cis Retinal,

Chem. Phys. Letters 31, 451-454 (1975),

by R. R. Birge, K. Schulten, and M. Karplus.

 

152.  Correlation Energy Contribution to the Ammonia Inversion Barrier,

Chem. Phys. Letters 31, 455-461 (1975),

by N. C. Dutta and M. Karplus.

 

153.  Semiclassical Trajectory Approach to Photoisomerization,

Chem. Phys. Letters 32, 11-17 (1975),

by A. Warshel and M. Karplus.

 

154.  Role of Structural Flexibility in Conformational Calculations.Application to

Acetylcholine and b-Methylacetylcholine,

J. Am. Chem. Soc. 97, 6996-7006 (1975),

by B. R. Gelin and M. Karplus.

 

155.  Comment: Reinterpretation of Hexatriene Spectrum and Comparison with Theory,

J. Chem. Phys. 63, 5507-5508 (1975),

by M. Karplus, R. M. Gavin, Jr., and S. A. Rice.

 

156.  Analysis of the Interaction of Organic Phosphates with Hemoglobin,

Biochemistry 15, 2869-2877 (1976),

by A. Szabo and M. Karplus.

 

157.  The Enumeration of Goldstone Diagrams in Many-Body Perturbation Theory,

J. Chem. Phys. 64, 1596-1603 (1976),

by P. J. Rossky and M. Karplus.

 

158.  Many-Body Perturbation Theory Applied to Molecules: Analysis and Correlation Energy

Calculation for Li2, N2, and H3,

J. Chem. Phys. 64, 2461-2659 (1976),

by D. L. Freeman and M. Karplus.

 

159.  The Calculation of One-Electron Properties from Xa Multiple Scattering Wavefunctions,

Chem. Phys. Letters 39, 33-38 (1976),

by D. A. Case and M. Karplus.

 

160.  Protein-folding Dynamics,

Nature 260, 404-406 (1976),

by M. Karplus and D. L. Weaver.

 

161.  Correlation Effects in the Spectra of Polyenes,

J. Chem. Phys. 64, 4422-4441 (1976),

by K. Schulten, I. Ohmine, and M. Karplus.

 

162.  Perturbation Theory and Ionic Models for Alkali Halide Systems. II. Dimers,

J. Chem. Phys. 64, 5165-5178 (1976),

by P. Brumer and M. Karplus.

 

163.  The Hinge-Bending Mode in Lysozyme,

Nature 262, 325-326 (1976),

by J. A. McCammon, B. R. Gelin, M. Karplus, and P. G. Wolynes.

 

164.  Dynamics of Folded Proteins,

Nature 267, 585-590 (1977),

by J. A. McCammon, B. R. Gelin, and M. Karplus.

 

165.  Mechanism of Tertiary Structural Change in Hemoglobin,

Proc. Natl. Acad. Sci. USA 74, 801-805 (1977),

by B. R. Gelin and M. Karplus.

 

166.  Nature of the Iron-Oxygen Bond in Oxyhemoglobin,

J. Am. Chem. Soc. 99, 6103-6105 (1977),

by B. H. Huynh, D. A. Case, and M. Karplus.

 

167.  Excitation Operators and the Extended Random-Phase Approximation. I. Theory,

Phys. Rev. A16, 807-821 (1977),

by A. C. Lasaga and M. Karplus.

 

168.  Convergence of the Valence-Bond Calculation for Methane,

Mol. Phys. 34, 1483-1492 (1977),

by M. Raimondi, W. Campion, and M. Karplus.

 

169.  Xa Multiple Scattering Calculations on Copper Porphine,

J. Am. Chem. Soc. 99, 6182-6194 (1977),

by D. A. Case and M. Karplus.

 

170.  Internal Motions of Antibody Molecules,

Nature 268, 765-766 (1977),

by J. A. McCammon and M. Karplus.

 

171.  Model Perturbation Theoretic Calculations with Finite Continuum Basis Sets,

J. Chem. Phys. 67, 5419-5427 (1977),

by P. J. Rossky and M. Karplus.

 

172.  Renormalized Configuration Interaction Method for Electron Correlation in the

Excited States of Polyenes,

J. Chem. Phys. 68, 2298-2318 (1978),

by I. Ohmine, M. Karplus, and K. Schulten.

 

173.  Stereochemistry of Carbon Monoxide Binding to Myoglobin and Hemoglobin,

J. Mol. Biol. 123, 697-701 (1978),

by D. A. Case and M. Karplus.

 

174.  Structural Aspects of Hemoglobin Function,

Biochemical and Clinical Aspects of Hemoglobin Abnormalities,

W. S. Caughey, editor, 515-525 (Academic Press, 1978),

by M. Karplus.

 

175.  Protein Structural Fluctuations During a Period of 100 ps,

Nature 277, 578 (1979),

by M. Karplus and J. A. McCammon.

 

176.  Picosecond Dynamics of Tyrosine Side Chains in Proteins,

Biochemistry 18, 927-942 (1979),

by J. A. McCammon, P. G. Wolynes, and M. Karplus.

 

177.  Side-Chain Torsional Potentials: Effect of Dipeptide, Protein, and Solvent Environment,

Biochemistry 18, 1256-1268 (1979),

by B. R. Gelin and M. Karplus.

 

178.  Solvation. A Molecular Dynamics Study of a Dipeptide in Water,

J. Am. Chem. Soc. 101, 1913-1937 (1979),

by P. J. Rossky and M. Karplus.

 

179.  A Model for the Simulation of an Aqueous Dipeptide Solution,

Biopolymers 18, 825-854 (1979),

by P. J. Rossky, M. Karplus, and A. Rahman.

 

180.  Diffusion-Collision Model for Protein Folding,

Biopolymers 18, 1421-1437 (1979),

by M. Karplus and D. L. Weaver.

 

181.  Excitation Operators and the Extended Random Phase Approximation. II. Applications,

J. Chem. Phys. 71, 1218-1234 (1979),

by A. C. Lasaga and M. Karplus.

 

182.  Diffusive Langevin Dynamics of Model Alkanes,

Chem. Phys. Letters 65, 4-11 (1979),

by R. M. Levy, M. Karplus, and J. A. McCammon.

 

183.  Binding of Oxygen and Carbon Monoxide to Hemoglobin. An Analysis of the

Ground and Excited States,

J. Am. Chem. Soc. 101, 4433-4453 (1979),

by D. A. Case, B. H. Huynh, and M. Karplus.

 

184.  Dynamics of Activated Processes in Globular Proteins,

Proc. Natl. Acad. Sci. USA 76, 3585-3589 (1979),

by J. A. McCammon and M. Karplus.

 

185.  Vibrational Approach to the Dynamics of an a-Helix,

Biopolymers 18, 2465-2495 (1979),

by R. M. Levy and M. Karplus.

 

186.  Dynamics of Ligand Binding to Heme Proteins,

J. Mol. Biol. 132, 343-368 (1979),

by D. A. Case and M. Karplus.

 

187.  Calculation of One-Electron Properties of LiH from Xa Multiple-Scattering Wave Functions,

J. Chem. Phys. 72, 7-19 (1980),

by M. Cook and M. Karplus.

 

188.  Generalized Perturbed Hartree-Fock Theory,

J. Chem. Phys. 72, 6085-6101 (1980),

by P. J. Rossky and M. Karplus.

 

189.  Solvation: A Molecular Dynamics Study of a Dipeptide in Water,

ACS Symposium Series 127, Water in Polymers, 23-42 (1980),

by M. Karplus and P. J. Rossky.

 

190.  Dynamics of Tyrosine Ring Rotations in a Globular Protein,

Biopolymers 19, 1375-1405 (1980),

by J. A. McCammon and M. Karplus.

 

191.  Molecular Dynamics of Ferrocytochrome c,

Nature 286, 304-305 (1980),

by S. H. Northrup, M. R. Pear, J. A. McCammon, and M. Karplus.

 

192.  Simulation of Protein Dynamics,

Ann. Rev. Phys. Chem. 31, 29-45 (1980),

by J. A. McCammon and M. Karplus.

 

193.  A Method for Constrained Energy Minimization of Macromolecules,

J. Comp. Chem. 1, 266-274 (1980),

by W. F. van Gunsteren and M. Karplus.

 

194.  Application of Xa Multiple-Scattering Theory to Planar Organic Molecules: One-Electron

Properties and Ionization Potentials of Benzene, Pyridine, Pyrazine, Pyrrole, and Imidazole,

J. Chem. Phys. 73, 3294-3313 (1980),

by D. A. Case, M. Cook, and M. Karplus.

 

195.  Proton NMR Studies of the Association and Folding of Glucagon in Solution,

FEBS Letters 119, 265-270 (1980),

by M. E. Wagman, C. M. Dobson, and M. Karplus.

 

196.  A Conformational Isomer of Bovine Pancreatic Trypsin Inhibitor Protein Produced by Refolding,

Nature 286, 630-632 (1980),

by D. J. States, C. M. Dobson, M. Karplus, and T. E. Creighton.

 

197.  Helix-Coil Transitions in a Simple Polypeptide Model,

Biopolymers 19, 2033-2045 (1980),

by J. A. McCammon, S. H. Northrup, M. Karplus, and R. M. Levy.

 

198.  Internal Mobility of Ferrocytochrome c,

Nature 287, 659-660 (1980),

by S. H. Northrup, M. R. Pear, J. A. McCammon, M. Karplus, and T. Takano.

 

199.  Photodynamics of Polyenes: The Effect of Electron Correlation on Potential Surfaces,

J. Chem. Phys. 73, 5230-5243 (1980),

by A. C. Lasaga, R. J. Aerni, and M. Karplus.

 

200.  Spin Dependent Properties of Perturbed Wave Functions: An Analytic Comparison of the

Exact, UHF, and Spin-Projected UHF States,

J. Chem. Phys. 73, 6196-6214 (1980),

by P. J. Rossky and M. Karplus.

 

201.  Molecular Dynamics Studies of NMR Relaxation in Proteins,

Biophys. J. 32, 628-630 (1980),

by R. M. Levy, M. Karplus, and J. A. McCammon.

 

202.  The Internal Dynamics of Globular Proteins, CRC

Crit. Rev. Biochem. 9, 293-350 (1981),

by M. Karplus and J. A. McCammon.

 

203.  Internal Dynamics of Proteins - Short Time and Long Time Motions of Aromatic Sidechains in PTI,

Biophys. J. 32, 603-618 (1980),

by M. Karplus, B. R. Gelin, and J. A. McCammon.

 

204.  Increase of 13C NMR Relaxation Times in Proteins due to Picosecond Motional Averaging,

J. Am. Chem. Soc. 103, 994-996 (1981),

by R. M. Levy, M. Karplus, and J. A. McCammon.

 

205.  Method for Estimating the Configurational Entropy of Macromolecules,

Macromolecules 14, 325-332 (1981),

by M. Karplus and J. N. Kushick.

 

206.  Solvation of a Dipeptide by Water,

Ann. NY Acad. Sci. 367, 151-161 (1981),

by M. Karplus and P. J. Rossky.

 

207.  Correlated Helix-Coil Transitions in Polypeptides,

Biopolymers 20, 629-632 (1981),

by M. R. Pear, S. H. Northrup, J. A. McCammon, M. Karplus, and R. M. Levy.

 

208.  Aspects of Protein Dynamics,

Ann. NY Acad. Sci. 367, 407-418 (1981),

by M. Karplus.

 

209.  Pressure Dependence of Aromatic Ring Rotations in Proteins: A Collisional Interpretation,

FEBS Letters 131, 34-36 (1981),

by M. Karplus and J. A. McCammon.

 

210.  Dynamics of Proteins,

Biomolecular Stereodynamics II, R. H. Sarma, editor, 211-228 (Adenine Press, New York, 1981),

by M. Karplus.

 

211.  NMR Relaxation Parameters in Molecules with Internal Motion: Exact Langevin

Trajectory Results Compared with Simplified Relaxation Models,

J. Am. Chem. Soc. 103, 5998-6011 (1981),

by R. M. Levy, M. Karplus, and P. G. Wolynes.

 

212.  Effect of Constraints, Solvent and Crystal Environment on Protein Dynamics,

Nature 293, 677-678 (1981),

by W. F. van Gunsteren and M. Karplus.

 

213.  The Calculation of Two-Electron Properties from Multiple-Scattering Xa Wavefunctions,

Chem. Phys. Letters 84, 565-570 (1981),

by M. Cook and M. Karplus.

 

214.  Molecular Dynamics of Ferrocytochrome c: Magnitude and Anisotropy of Atomic Displacements,

J. Mol. Biol. 153, 1087-1109 (1981),

by S. H. Northrup, M. R. Pear, J. D. Morgan, J. A. McCammon, and M. Karplus.

 

215.  Molecular Dynamics of an a-Helical Polypeptide: Temperature Dependence and

Deviation from Harmonic Behavior,

Proc. Natl. Acad. Sci. USA 79, 1346-1350 (1982),

by R. M. Levy, D. Perahia, and M. Karplus.

 

216.  Fluctuations and Averaging of Proton Chemical Shifts in the Bovine Pancreatic Trypsin Inhibitor,

Biochemistry 21, 1118-1125 (1982), by

J. C. Hoch, C. M. Dobson, and M. Karplus.

 

217.  Correlation Effects in the Excited States of Polydiacetylene Models,

Chem. Phys. Letters 88, 171-176 (1982),

by U. Dinur and M. Karplus.

 

218.  Protein Dynamics in Solution and in a Crystalline Environment: A Molecular Dynamics Study,

Biochemistry 21, 2259-2274 (1982),

by W. F. van Gunsteren and M. Karplus.

 

219.  Dynamics of Proteins,

Berichte der Bunsen-Gesellschaft f¸r Physikalische Chemie 86, 386-395 (1982),

by M. Karplus.

 

220.  Dipolar NMR Relaxation of Nonprotonated Aromatic Carbons in Proteins:

Structural and Dynamical Effects,

Biophys. J. 39, 107-113 (1982),

by R. M. Levy, C. M. Dobson, and M. Karplus.

 

221.  Dynamical Theory of Activated Processes in Globular Proteins,

Proc. Natl. Acad. Sci. USA 79, 4035-4039 (1982),

by S. H. Northrup, M. R. Pear, C.-Y. Lee, J. A. McCammon, and M. Karplus.

 

222.  Extended Wave Packet Dynamics: Exact Solution for Collinear Atom, Diatomic Molecule Scattering,

Chem. Phys. Letters 90, 301-305 (1982),

by R. D. Coalson and M. Karplus.

 

223.  Time Dependence of Atomic Fluctuations in Proteins: Analysis of Local and Collective Motions in

Bovine Pancreatic Trypsin Inhibitor,

Biochemistry 21, 5230-5241 (1982),

by S. Swaminathan, T. Ichiye, W. F. van Gunsteren, and M. Karplus.

 

224.  Heme-Iron Ligand Binding,

Hemoglobin and Oxygen Binding, C. Ho, editor, 3-11 (Elsevier North Holland, Inc., 1982),

by M. Karplus.

 

225.  Effect of Constraints on the Dynamics of Macromolecules,

Macromolecules 15, 1528-1544 (1982),

by W. F. van Gunsteren and M. Karplus.

 

226.  Dynamics of Proteins,

Structure, Dynamics, Interactions and Evolution of Biological Macromolecules,

C. HÈlËne, editor, 253-269 (D. Reidel Publishing Co., 1983),

by M. Karplus.

 

227.  Equilibrium Geometry and Dynamics of the Valence Excited States of 1,3-Butadiene,

J. Chem. Phys. 87, 924-932 (1983),

by U. Dinur, R. J. Hemley, and M. Karplus.

 

228.  CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations,

J. Comput. Chem. 4, 187-217 (1983),

by B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus.

 

229.  Dynamics of Proteins: Elements and Function,

Ann. Rev. Biochem. 53, 263-300 (1983),

by M. Karplus and J. A. McCammon.

 

230.  Fluorescence Depolarization of Tryptophan Residues in Proteins: A Molecular Dynamics Study,

Biochemistry 22, 2884-2893 (1983),

by T. Ichiye and M. Karplus.

 

231.  Trajectory Studies of NMR Relaxation in Flexible Molecules,

ACS Advances in Chemistry Series: Molecular-Based Study of Fluids,

J. M. Haile and G. A. Mansoori, editors, 445-468 (American Chemical Society, 1983),

by R. M. Levy and M. Karplus.

 

232.  The Dynamic Picture of Protein Structure,

Acc. Chem. Res. 16, 187-193 (1983),

by J. A. McCammon and M. Karplus.

 

233.  Solution NMR Studies of Intact Lambda Repressor,

J. Biomolecular Struc. & Dynamics 1, 151-157 (1983),

by M. A. Weiss, D. J. Patel, R. T. Sauer, and M. Karplus.

 

234.  Dynamics of DNA Oligomers,

J. Biomolecular Struc. & Dynamics 1, 231-252 (1983),

by B. Tidor, K. K. Irikura, B. R. Brooks, and M. Karplus.

 

235.  Xa Multiple-Scattering Calculations on Iron (II) Porphine,

J. Chem. Phys. 79, 2881-2892 (1983),

by S. F. Sontum, D. A. Case, and M. Karplus.

 

236.  Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in

Bovine Pancreatic Trypsin Inhibitor,

Proc. Natl. Acad. Sci. USA 80, 6571-6575 (1983),

by B. R. Brooks and M. Karplus.

 

237.  Deformable Stochastic Boundaries in Molecular Dynamics,

J. Chem. Phys. 79, 6312-6325 (1983),

by C. L. Brooks III and M. Karplus.

 

238.  Generalized Quantum Liouville Equation: Its Solution by Wave Packet Dynamics,

J. Chem. Phys. 79, 6150-6161 (1983),

by R. D. Coalson and M. Karplus.

 

239.  Structure-Specific Model of Hemoglobin Cooperativity,

Proc. Natl. Acad. Sci. USA 80, 7055-7059 (1983),

by A. W. Lee and M. Karplus.

 

240.  Molecular Anatomy of the Antibody Binding Site,

J. Biol. Chem. 258, 14433-14437 (1983),

by J. Novotny, R. E. Bruccoleri, J. Newell, D. Murphy, E. Haber, and M. Karplus.

 

241.  Hemoglobin Tertiary Structural Change on Ligand Binding: Its Role in the Co-operative Mechanism,

J. Mol. Biol. 171, 489-559 (1983),

by B. R. Gelin, A. W.-M. Lee, and M. Karplus.

 

242.  Local and Collective Motions in Protein Dynamics,

Mobility and Function in Proteins and Nucleic Acids,

Ciba Foundation Symposium 93, 271-283 (Pitman Books Ltd., London, 1983),

by S. Swaminathan, T. Ichiye, W. F. van Gunsteren, and M. Karplus.

 

243.  Two Dimensional 1H NMR Study of the l Operator Site OL1:

A Sequential Assignment Strategy and its Application,

Proc. Natl. Acad. Sci. USA 81, 130-134 (1984),

by M. A. Weiss, D. J. Patel, R. T. Sauer, and M. Karplus.

 

244.  Vibrational Analysis of the Lowest 1Bu+ State of trans, trans 1,3,5,7-octatetraene,

J. Chem. Phys. 80, 23-30 (1984),

by B. E. Kohler, T. A. Spiglanin, R. J. Hemley, and M. Karplus.

 

245.  Stochastic Boundary Conditions for Molecular Dynamics Simulations of ST2 Water,

Chem. Phys. Letters 105, 495-500 (1984),

by A. T. Br¸nger, C. L. Brooks III, and M. Karplus.

 

246.  Motional Averaging of Proton Nuclear Overhauser Effects in Proteins.

Predictions from a Molecular Dynamics Simulation of Lysozyme,

J. Am. Chem. Soc. 106, 1923-1930 (1984),

by E. T. Olejniczak, C. M. Dobson, R. M. Levy, and M. Karplus.

 

247.  A New Two-Disulphide Intermediate in the Refolding of Reduced Bovine Pancreatic Trypsin Inhibitor,

J. Mol. Biol. 174, 411-418 (1984),

by D. J. States, C. M. Dobson, T. E. Creighton, and M. Karplus.

 

248.  1H-NMR Study of the l Operator Site OL1: Assignment of the Imino and Adenine H2 Resonances,

Nucleic Acids Research 12, 4035-4047 (1984),

by M. A. Weiss, D. J. Patel, R. T. Sauer, and M. Karplus.

 

249.  NMR Characterization of DNA: Assignment of Major Groove Sugar Protons

of the l-Phage Operator Site OL1 by Two-Dimensional NOE and J-Correlated Spectra,

J. Am. Chem. Soc. 106, 4269-4270 (1984),

by M. A. Weiss, D. J. Patel, R. T. Sauer, and M. Karplus.

 

250.  Diffusion-Collision Model for the Folding Kinetics of the l-Repressor Operator-Binding Domain,

J. Biomol. Struct. Dyns. 1, 1243-1255 (1984),

by D. Bashford, D. L. Weaver, and M. Karplus.

 

251.  New Sum Rules for Electronic Absorption Spectra,

J. Chem. Phys. 81, 2891-2896 (1984),

by R. D. Coalson and M. Karplus.

 

252.  Evaluation of the Configurational Entropy for Proteins: Application to Molecular Dynamics

Simulations of an a-Helix,

Macromolecules 17, 1370-1374 (1984),

by R. M. Levy, J. Kushick, D. Perahia, and M. Karplus.

 

253.  Amino-Terminal Arm of the l Repressor: A 1H NMR Study,

Biochemistry 23, 5090-5095 (1984),

by M. A. Weiss, R. T. Sauer, D. J. Patel, and M. Karplus.

 

254.  An Analysis of Incorrectly Folded Protein Models: Implications for Structure Predictions,

J. Mol. Biol. 177, 787-818 (1984),

by J. Novotny, R. E. Bruccoleri, and M. Karplus.

 

255.  Brownian Dynamics Simulations: Statistical Error of Correlation Functions,

J. Chem. Phys. 81, 6106-6118 (1984),

by S. Lee and M. Karplus.

 

256.  Dynamics of Proteins,

Adv. Biophys. 18, 165-190 (1984),

by M. Karplus.

 

257.  The Temperature Dependence of Protein Structure and Mobility,

Transactns. Amer. Crystallographic Assoc. 20, 109-122 (1984),

by D. Ringe, J. Kuriyan, G. A. Petsko, M. Karplus, H. Frauenfelder, R. F. Tilton, and I. D. Kuntz.

 

258.  Electronic Structure of the MoFe3S4(SH)63-Ion,

J. Am. Chem. Soc. 107, 257-259 (1985),

by M. Cook and M. Karplus.

 

259.  Solution Conformation of a Heptadecapeptide Comprising the DNA Binding Helix F of the

Cyclic AMP Receptor Protein of Escherichia coli: Combined Use of 1H Nuclear Magnetic Resonance

and Restrained Molecular Dynamics,

J. Mol. Biol. 186, 435-455 (1985),

by G. M. Clore, A. M. Gronenborn, A. T. Br¸nger, and M. Karplus.

 

260.  Theoretical Study of the Ground and Excited Singlet States of Styrene,

J. Am. Chem. Soc. 107, 836-844 (1985),

by R. J. Hemley, U. Dinur, V. Vaida, and M. Karplus.

 

261.  Role of Electrostatics in the Structure, Energy, and Dynamics of Biomolecules:

A Model Study of N-Methylalanylacetamide,

J. Am. Chem. Soc. 107, 1166-1173 (1985),

by B. M. Pettitt and M. Karplus.

 

262.  Construction of a Model for the Three-Dimensional Structure of Human Renal Renin,

Hypertension 7, 13-26 (1985),

by W. Carlson, M. Karplus, and E. Haber.

 

263.  Structure of Proteins with Single-Site Mutations: A Minimum Perturbation Approach,

Proc. Natl. Acad. Sci. USA 82, 1697-1700 (1985),

by H. H.-L. Shih, J. Brady, and M. Karplus.

 

264.  Active Site Dynamics in Protein Molecules: A Stochastic Boundary Molecular-Dynamics Approach,

Biopolymers 24, 843-865 (1985),

by C. L. Brooks III, A. T. Br¸nger, and M. Karplus.

 

265.  The Singlet States of Styrene. Theoretical Vibrational Analysis of the Ultraviolet Spectrum,

J. Chem. Phys. 82, 5379-5397 (1985),

by R. J. Hemley, D. G. Leopold, V. Vaida, and M. Karplus.

 

266.  Restraints in Temperature-Factor Refinement for Macromolecules:

An Evaluation by Molecular Dynamics,

Acta Cryst. B41, 191-201 (1985),

by H.-A. Yu, M. Karplus, and W. A. Hendrickson.

 

267.  The Potential of Mean Force Between Polyatomic Molecules in Polar Molecular Solvents,

J. Chem. Phys. 83, 781-789 (1985),

by B. M. Pettitt and M. Karplus.

 

268.  Dynamic Aspects of Protein Structure,

Ann. NY Acad. Sci. 439, 107-123 (1985),

by M. Karplus.

 

269.  Vicinal Coupling Constants and Protein Dynamics,

Biochemistry 24, 3831-3841 (1985),

by J. C. Hoch, C. M. Dobson, and M. Karplus.

 

270.  Normal Modes for Specific Motions of Macromolecules: Application to the

Hinge-Bending Mode of Lysozyme,

Proc. Natl. Acad. Sci. USA 82, 4995-4999 (1985),

by B. R. Brooks and M. Karplus.

 

271.  Transition from B to Z DNA: Contribution of Internal Fluctuations to the Configurational Entropy

Difference,

Science 229, 571-572 (1985),

by K. K. Irikura, B. Tidor, B. R. Brooks, and M. Karplus.

 

272.  Molecular Dynamics of Myoglobin at 298∞K: Results from a 300 ps Computer Simulation,

Biophys. J. 48, 509-518 (1985),

by R. M. Levy, R. P. Sheridan, J. W. Keepers, G. S. Dubey, S. Swaminathan, and M. Karplus.

 

273.  Configuration Entropy of the Alanine Dipeptide in Vacuum and in Solution:

A Molecular Dynamics Study,

J. Am. Chem. Soc. 107, 6103-6105 (1985),

by J. Brady, and M. Karplus.

 

274.  The Potential of Mean Force Surface for the Alanine Dipeptide in Aqueous Solution:

A Theoretical Approach,

Chem. Phys. Letters 121, 194-201 (1985),

by B. M. Pettitt and M. Karplus.

 

275.  Domain Association in Immunoglobulin Molecules: The Packing of Variable Domains,

J. Mol. Biol. 186, 651-663 (1985),

by C. Chothia, J. Novotny, R. E. Bruccoleri, and M. Karplus.

 

276.  Structural and Energetic Effects of Truncating Long Ranged Interactions in Ionic and Polar Fluids,

J. Chem. Phys. 83, 5897-5908 (1985),

by C. L. Brooks III, B. M. Pettitt, and M. Karplus.

 

277.  Chain Closure with Bond Angle Variations,

Macromolecules 18, 2767-2773 (1985),

by R. E. Bruccoleri, and M. Karplus.

 

278.  Active Site Dynamics of Ribonuclease,

Proc. Natl. Acad. Sci. USA 82, 8458-8462 (1985),

by A. T. Br¸nger, C. L. Brooks III, and M. Karplus.

 

279.  Electronic Structure of the MoFe3S4(SH)63-Ion: A Broken-Symmetry Metal-Sulfur Cluster,

J. Chem. Phys. 83, 6344-6366 (1985),

by M. Cook and M. Karplus.

 

280.  Molecular Dynamics of Biomolecules: An Introductory Overview,

Molecular Dynamics and Protein Structure,

J. Hermans, editor, 1-2 (Proceedings of Workshop at U. North Carolina, 1985),

by M. Karplus.

 

281.  Molecular Dynamics with Stochastic Boundaries: Application to the Active Site of Proteins in

Solution,

Molecular Dynamics and Protein Structure,

J. Hermans, editor, 16-17 (Proceedings of Workshop at U. North Carolina, 1985),

by A. T. Br¸nger, C. L. Brooks III, and M. Karplus.

 

282.  Entropy of Macromolecules,

Molecular Dynamics and Protein Structure,

J. Hermans, editor, 47-49 (Proceedings of Workshop at U. North Carolina, 1985),

by M. Karplus, J. Brady, B. R. Brooks, J. Kushick, and B. M. Pettitt.

 

283.  Incorrectly Folded Protein Models: Studies by Energy Minimization and Quenched Dynamics,

Molecular Dynamics and Protein Structure,

J. Hermans, editor, 156-160 (Proceedings of Workshop at U. North Carolina, 1985),

by J. Novotny, B. E. Bruccoleri, and M. Karplus.

 

284.  Molecular Dynamics Simulation of the Anticodon Arm of Phenylalanine Transfer RNA,

Proceedings of the NATO Advanced Research Workshop,

P. van Knippenberg and C. W. Hilbers, editors (Plenum Press, 1985),

by L. Nilsson and M. Karplus.

 

285.  Protein-Protein Interactions in DNA Recognition. Proton Nuclear Magnetic Resonance Studies of

±l cI Repressors Genetically Altered by Site-Directed Mutagenesis,

Biophys. J. 49, 29-33 (1986),

by M. A. Weiss, R. Stearman, A. Jeitler-Nilsson, M. Karplus, and R. T. Sauer.

 

286.  Low-Frequency Modes in Proteins: Use of the Effective-Medium Approximation to Interpret the

Fractal Dimension Observed in Electron-Spin Relaxation Measurements,

Phys. Rev. Letters 56, 394-397 (1986),

by R. Elber and M. Karplus.

 

287.  The Dynamics of Proteins,

Scientific American 254, 42-51 (1986),

by M. Karplus and J. A. McCammon.

 

288.  Spatially Constrained Minimization of Macromolecules,

J. Comp. Chem. 7, 165-175 (1986),

by R. E. Bruccoleri, and M. Karplus.

 

289.  Low Frequency Dynamics of Proteins Studied by Neutron Time-of-Flight Spectroscopy,

Physica 136B, 256-259 (1986),

by S. Cusack, J. Smith, J. Finney, M. Karplus, and J. Trewhella.

 

290.  Structure Refinement of Oligonucleotides by Molecular Dynamics with Nuclear Overhauser Effect

Interproton Distance Restraints: Application to 5¢ d(C-G-T-A-C-G)2,

J. Mol. Biol. 188, 455-475 (1986),

by L. Nilsson, G. M. Clore, A. M. Gronenborn, A. T. Br¸nger, and M. Karplus.

 

291.  Genetic Methods in High-Resolution NMR Studies of Proteins,

NMR in the Life Sciences, E. M. Bradbury and C. Nicolini, editors, 37-48

(Plenum Publishing Corp., 1986),

by M. A. Weiss, A. Jeitler-Nilsson, N. J. Fischbein, M. Karplus, and R. T. Sauer.

 

292.  Effect of Anisotropy and Anharmonicity on Protein Crystallographic Refinement: An Evaluation by

Molecular Dynamics,

J. Mol. Biol. 190, 227-254 (1986),

by J. Kuriyan, G. A. Petsko, R. M. Levy, and M. Karplus.

 

293.  Molecular Dynamics Simulations of Native and Substrate-bound Lysozyme,

J. Mol. Biol. 190, 455-479 (1986),

by C. B. Post, B. R. Brooks, M. Karplus, C. M. Dobson, P. J. Artymiuk, J. C. Cheetham, and

D. C. Phillips.

 

294.  Does Lysozyme Follow the Lysozyme Pathway? An Alternative Based on Dynamic, Structural, and

Stereoelectronic Considerations,

J. Am. Chem. Soc. 108, 1317-1319 (1986),

by C. B. Post and M. Karplus.

 

295.  Three-Dimensional Structure of Proteins Determined by Molecular Dynamics with Interproton

Distance Restraints: Application to Crambin,

Proc. Natl. Acad. Sci. USA 83, 3801-3805 (1986),

by A. T. Br¸nger, G. M. Clore, A. M. Gronenborn, and M. Karplus.

 

296.  Inelastic Neutron Scattering Analysis of Low Frequency Motion in Proteins: A Normal Mode Study

of the Bovine Pancreatic Trypsin Inhibitor,

J. Chem. Phys. 85, 3636-3654 (1986),

by J. Smith, S. Cusack, U. Pezzeca, B. R. Brooks, and M. Karplus.

 

297.  Application of Molecular Dynamics with Interproton Distance Restraints to Three-Dimensional

Protein Structure Determination. A Model Study of Crambin,

J. Mol. Biol. 191, 523-551 (1986),

by G. M. Clore, A. T. Br¸nger, M. Karplus, and A. M. Gronenborn.

 

298.  Dynamics of Ligand Binding to Proteins,

Design and Synthesis of Organic Molecules Based on Molecular Recognition, G. Van Binst, editor, 81-102 (Proc. XVIIIth Solvay Conference on Chemistry, 1983; Springer-Verlag Berlin, 1986),

by M. Karplus.

 

299.  Theoretical Approaches to Solvation of Biopolymers,

Methods in Enzymology 127, L. Packer, editor, 369-400 (Academic Press, Inc., 1986),

by C. L. Brooks III and M. Karplus.

 

300.  X-ray Structure and Refinement of Carbon-monoxy (Fe II)-myoglobin at 1.5 ≈ Resolution,

J. Mol. Biol. 192, 133-154 (1986),

by J. Kuriyan, S. Wilz, M. Karplus, and G. A. Petsko.

 

301.  Crystallographic Studies of Enzyme-Substrate Complexes (and Other Things) at Low Temperature,

Structural Biological Applications of X-ray Absorption, Scattering and Diffraction,

H. D. Bartunik and B. Chance, editors, 99-109 (8th International Biophysics Congress, 1984; Academic Press, Inc., 1986),

by G. A. Petsko, J. Kuriyan, W. A. Gilbert, D. Ringe, and M. Karplus.

 

302.  The Hinge-Bending Mode of a Lysozyme-Inhibitor Complex,

Biopolymers 25, 1767-1802 (1986),

by R. E. Bruccoleri, M. Karplus, and J. A. McCammon.

 

303.  Structure and Internal Mobility of Proteins: A Molecular Dynamics Study of Hen Egg White Lysozyme,

Biopolymers 25, 1909-1939 (1986),

by T. Ichiye, B. D. Olafson, S. Swaminathan, and M. Karplus.

 

304.  Theoretical Study of the Ground-State Vibrations of the Linear Polyenes,

J. Chem. Phys. 85, 6550-6564 (1986),

by R. J. Hemley, B. R. Brooks, and M. Karplus.

 

305.  Interaction Energies: Their Role in Drug Design,

Molecular Graphics and Drug Design, A.S.V. Burgen, G.C.K. Roberts, and M. S. Tute, editors,

75-113 (Elsevier Science Publishers, 1986),

by B. M. Pettitt and M. Karplus.

 

306.  Empirical Energy Functions for Energy Minimization and Dynamics of Nucleic Acids,

J. Comp. Chem. 7, 591-616 (1986),

by L. Nilsson and M. Karplus.

 

307.  Integral Equation Model for Aqueous Solvation of Polyatomic Solutes: Application to the

Determination of the Free Energy Surface for the Internal Motion of Biomolecules,

J. Phys. Chem. 90, 6335-6345 (1986),

by B. M. Pettitt, M. Karplus, and P. J. Rossky.

 

308.  The Three-Dimensional Structure of a 1-purothionin in Solution: Combined Use of Nuclear Magnetic

Resonance, Distance Geometry and Restrained Molecular Dynamics,

EMBO 5, 2729-2735 (1986),

by G. M. Clore, M. Nilges, D. K. Sukumaran, A. T. Br¸nger, M. Karplus, and A. M. Gronenborn.

 

309.  Interdomain Motion in Liver Alcohol Dehydrogenase: Structural and Energetic Analysis of the

Hinge Bending Mode,

J. Biol. Chem. 261, 15273-15280 (1986),

by F. Colonna-Cesari, D. Perahia, M. Karplus, H. Ecklund, C. I. Br‰ndÈn, and O. Tapia.

 

310.  Internal Dynamics of Proteins,

Methods in Enzymology 131, C.H.W. Hirs and S. N. Timasheff, editors, 283-307

(Academic Press, Inc., 1986),

by M. Karplus.

 

311.  Internal Motion of Proteins: Nuclear Magnetic Resonance Measurements and Dynamic Simulations,

Methods in Enzymology 131, C.H.W. Hirs and S. N. Timasheff, editors, 362-389

(Academic Press, Inc., 1986),

by C. M. Dobson and M. Karplus. 

 

312.  Role of Active Site Residues and Solvation in RNase A,

Ann. NY Acad. Sci. 471, reprinted from International Symposium on Bioorganic Chemistry, R. Breslow, editor, 295-298 (1986),

by C. L. Brooks III, A. T. Br¸nger, M. Francl, K. Haydock, L. C. Allen, and M. Karplus.

 

313.  Molecular Dynamics of Biomolecules: Overview and Applications,

Isr. J. Chem. 27, 121-126 (1986),

by M. Karplus.

 

314.  Electron Correlation and Density-Functional Methods,

J. Phys. Chem. 91, 31-37 (1987),

M. Cook and M. Karplus.

 

315.  Prediction of the Folding of Short Polypeptide Segments by Uniform Conformational Sampling,

Biopolymers 26, 137-168 (1987),

by R. E. Bruccoleri and M. Karplus.

 

316.  Thermal Expansion of a Protein,

Biochemistry 26, 254-261 (1987),

by H. Frauenfelder, H. Hartmann, M. Karplus, I. D. Kuntz, Jr., J. Kuriyan, F. Parak, G. A. Petsko, D. Ringe, R. F. Tilton, Jr., M. L. Connolly, and N. Max.

 

317.  Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin,

Science 235, 318-321 (1987),

by R. Elber and M. Karplus.

 

318.  Crystallographic R Factor Refinement by Molecular Dynamics,

Science 235, 458-460 (1987),

by A. T. Br¸nger, J. Kuriyan, and M. Karplus.

 

319.  1H NMR Aromatic Spectrum of the Operator Binding Domain of the l Repressor:

Resonance Assignment with Application to Structure and Dynamics,

Biochemistry 26, 890-897 (1987),

by M. A. Weiss, M. Karplus, and R. T. Sauer.

 

320.  Dimerization of the Operator Binding Domain of Phage l Repressor,

Biochemistry 26, 897-904 (1987),

by M. A. Weiss, C. O. Pabo, M. Karplus, and R. T. Sauer.

 

321.  Solution of a Protein Crystal Structure with a Model Obtained from NMR Interproton

Distance Restraints,

Science 235, 1049-1053 (1987),

by A. T. Br¸nger, R. L. Campbell, G. M. Clore, A. M. Gronenborn, M. Karplus, G. A. Petsko, and M. M. Teeter.

 

322.  Kinetics of Diffusion-Influenced Bimolecular Reactions in Solution. I. General Formalism and

Relaxation Kinetics of Fast Reversible Reactions,

J. Chem. Phys. 86, 1883-1903 (1987),

by S. Lee and M. Karplus.

 

323.  Kinetics of Diffusion-Influenced Bimolecular Reactions in Solution. II. Effects of the Gating Mode

and Orientation-Dependent Reactivity,

J. Chem. Phys. 86, 1904-1921 (1987),

by S. Lee and M. Karplus.

 

324.  Brownian Dynamics Simulation of Protein Folding: A Study of the Diffusion-Collision Model,

Biopolymers 26, 481-506 (1987),

by S. Lee, M. Karplus, D. Bashford, and D. Weaver.

 

325.  A Comparison of the Restrained Molecular Dynamics and Distance Geometry Methods for

Determining Three-Dimensional Structures of Proteins on the Basis of Interproton Distances,

FEBS 213, 269-277 (1987),

by G. M. Clore, M. Nilges, A. T. Br¸nger, M. Karplus, and A. M. Gronenborn.

 

326.  Models for the Three-Dimensional Structure of Renin Inhibitors Bound in the Active Site of

Human Renin: An Analysis of the Properties that Produce Tight Binding,

J. Cardiovascular Pharmacology 10, S91-S93 (1987),

by W. D. Carlson, M. Handschumacher, N. Summers, M. Karplus, and E. Haber.

 

327.  Molecular Dynamics: Applications to Proteins,

Ann. NY Acad. Sci. 482, 255-266 (1987),

by M. Karplus.

 

328.  The Prediction and Analysis of Mutant Structures,

Protein Engineering, D. L. Oxender and C. F. Fox, editors, 35-44 (Alan R. Liss, Inc., 1987),

by M. Karplus.

 

329.  Conformations of Intermediates in the Folding of the Pancreatic Trypsin Inhibitor,

J. Mol. Biol. 195, 731-739 (1987),

by D. J. States, T. E. Creighton, C. M. Dobson, and M. Karplus.

 

330.  Estimation of Uncertainties in X-Ray Refinement Results by Use of Perturbed Structures,

Proteins 2, 1-12 (1987),

by J. Kuriyan, M. Karplus, and G. A. Petsko.

 

331.  The Structure of Water Surrounding a Peptide: A Theoretical Approach,

Chem. Phys. Lett. 136, 383-386 (1987),

by B. M. Pettitt and M. Karplus.

 

332.  Molecular Dynamics: Applications to Proteins,

Cold Spring Harbor Symposia on Quantitative Biology LII, 381-390 (1987),

by M. Karplus, A. T. Br¸nger, R. Elber, and J. Kuriyan.

 

333.  Anisotropy and Anharmonicity of Atomic Fluctuations in Proteins: Analysis of a

Molecular Dynamics Simulation,

Proteins 2, 236-259 (1987),

by T. Ichiye and M. Karplus.

 

334.  Free Energy Perturbation Method for Chemical Reactions in the Condensed Phase:

A Dynamical Approach Based on a Combined Quantum and Molecular Mechanics Potential,

J. Am. Chem. Soc. 109, 8092-8094 (1987),

by P. A. Bash, M. J. Field, and M. Karplus.

 

335.  Trypsinogen-Trypsin Transition: A Molecular Dynamics Study of Induced Conformational Change in

the Activation Domain,

Biochemistry 26, 5153-5162 (1987),

by A. T. Br¸nger, R. Huber, and M. Karplus.

 

336.  A Method for Determining Reaction Paths in Large Molecules: Application to Myoglobin,

Chem. Phys. Lett. 139, 375-380 (1987),

by R. Elber and M. Karplus.

 

337.  Analysis of Sidechain Orientations in Homologous Proteins,

J. Mol. Biol. 196, 175-198 (1987),

by N. L. Summers, W. D. Carlson, and M. Karplus.

 

338.  Electrostatic Effects and Hydrogen Exchange Behaviour in Proteins. The pH Dependence of

Exchange Rates in Lysozyme,

J. Mol. Biol. 197, 111-122 (1987),

by M. Delepierre, C. M. Dobson, M. Karplus, F. M. Poulsen, D. J. States, and R. E. Wedin.  Appendix: A Model for Electrostatic Effects in Proteins, 122-130, by D. J. States and M. Karplus.

 

339.  Refinement of the Solution Structure of the DNA Hexamer 5¢ d(GCATGC)2: Combined Use of

Nuclear Magnetic Resonance and Restrained Molecular Dynamics,

Biochemistry 26, 3718-3733 (1987),

by M. Nilges, G. M. Clore, A. M. Gronenborn, A. T. Br¸nger, M. Karplus, and L. Nilsson.

 

340.  Molecular Dynamics Simulations of Proteins,

Physics Today 40, 68-72 (1987),

by M. Karplus.

 

341.  Quaternary Structure and Function in Phage l Repressor: 1H-NMR Studies of Genetically Altered

Proteins,

J. Biomolecular Struc. & Dyn. 5, 539-556 (1987),

by M. A. Weiss, M. Karplus, and R. T. Sauer.

 

342.  Solution Conformations of Human Growth Hormone Releasing Factor: Comparison of the Restrained

Molecular Dynamics and Distance Geometry Methods for a System Without Long-Range Distance Data,

Protein Engineering 1, 399-406 (1987),

by A. T. Br¸nger, G. M. Clore, A. M. Gronenborn, and M. Karplus.

 

343.  Molecular and Stochastic Dynamics of Proteins,

Proc. Natl. Acad. Sci. USA 84, 7933-7937 (1987),

by W. Nadler, A. T. Br¸nger, K. Schulten, and M. Karplus.

 

344.  Configurational Entropy of Native Proteins,

Biophys. J. 52, 1083-1085 (1987),

by M. Karplus, T. Ichiye, and B. M. Pettitt.

 

345.  Molecular Dynamics: Applications to Proteins,

Structure & Expression I, R. H. Sarma and M. H. Sarma, editors, 55-65 (Adenine Press, 1988),

by M. Karplus, A. T. Br¸nger, R. Elber, and J. Kuriyan.

 

346.  Theoretical Analysis of the 11Bu+ (1B1+) ¨ 11Ag- (1A1-) Transition of trans- and cis-1,3,5-Hexatriene,

J. Phys. Chem. 92, 945-954 (1988),

by R. J. Hemley, A. C. Lasaga, V. Vaida, and M. Karplus.

 

347.  Dynamics of Reactions Involving Diffusive Multidimensional Barrier Crossing,

J. Phys. Chem. 92, 1075-1086 (1988),

by S. Lee and M. Karplus.

 

348.  Analysis of Proton Release in Oxygen Binding by Hemoglobin: Implications for the

Cooperative Mechanism,

Biochemistry 27, 1285-1301 (1988),

by A. W. Lee, M. Karplus, C. Poyart, and E. Bursaux.

 

349.  The Normal Modes of the Gramicidin-A Dimer Channel,

Biophys. J. 53, 297-309 (1988),

by B. Roux and M. Karplus.

 

350.  Parametrization of the Friction Constant for Stochastic Simulations of Polymers,

J. Phys. Chem. 92, 2636-2641 (1988),

by R. W. Pastor and M. Karplus.

 

351.  Anisotropy and Anharmonicity of Atomic Fluctuations in Proteins: Implications for X-ray Analysis,

Biochemistry 27, 3487-3497 (1988),

by T. Ichiye and M. Karplus.

 

352.  The Conformational Properties of the Delta Opioid Peptide [D-Pen2,D-Pen5] enkephalin in

Aqueous Solution Determined by NMR and Energy Minimization Calculations,

J. Am. Chem. Soc. 110, 3351-3359 (1988),

by V. J. Hruby, L.-F. Kao, B. M. Pettitt, and M. Karplus.

 

353.  Conformational Free Energy of Hydration for the Alanine Dipeptide: Thermodynamic Analysis,

J. Phys. Chem. 92, 3994-3997 (1988),

by B. M. Pettitt and M. Karplus.

 

354.  Brownian Dynamics Simulation of a Lipid Chain in a Membrane Bilayer,

J. Chem. Phys. 89, 1112-1127 (1988),

R. W. Pastor, R. M. Venable, and M. Karplus.

 

355.  A Simulation Based Model of NMR T1 Relaxation in Lipid Bilayer Vesicles,

J. Chem. Phys. 89, 1128-1140 (1988),

by R. W. Pastor, R. M. Venable, M. Karplus, and A. Szabo.

 

356.  A Thermodynamic Analysis of Solvation,

J. Chem. Phys. 89, 2366-2379 (1988),

by H.-A. Yu and M. Karplus.  

 

357.  Inelastic Neutron Scattering Analysis of Picosecond Internal Protein Dynamics.

Comparison of Harmonic Theory with Experiment,

J. Mol. Biol. 202, 903-908 (1988),

by S. Cusack, J. Smith, J. Finney, B. Tidor, and M. Karplus.

 

358.  Dynamics Simulation Studies of Apoazurin of Alcaligenes denitrificans,

Biochemistry 27, 6908-6921 (1988),

by L.X.-Q. Chen, R. A. Engh, A. T. Br¸nger, D. T. Nguyen, M. Karplus, and G. R. Fleming.

 

359.  Electrostatic Effects of Charge Perturbations Introduced by Metal Oxidation in Proteins.

A Theoretical Analysis,

J. Mol. Biol. 203, 507-510 (1988),

by D. Bashford, M. Karplus, and G. W. Canters.

 

360.  Proteins: Dynamics and Function,

Biotechnology and the Human Genome. Innovations and Impact 46,

A. D. Woodhead and B. J. Barnhart, editors, 57-61 (Plenum Press, 1988),

by M. Karplus.

 

361.  Ab Initio Force Field for the Planar Vibrations of Benzene,

J. Chem. Phys. 89, 4235-4245 (1988),

by H. Guo and M. Karplus.

 

362.  Polar Hydrogen Positions in Proteins: Empirical Energy Placement and Neutron

Diffraction Comparison,

Proteins: Structure, Function & Genetics 4, 148-156 (1988),

by A. T. Br¸nger and M. Karplus.

 

363.  Diffusion-Collision Model for the Folding Kinetics of Myoglobin,

Proteins 4, 211-227 (1988),

by D. Bashford, F. E. Cohen, M. Karplus, I. D. Kuntz, and D. L. Weaver.

 

364.  Guanidinium as a Probe of the Gramicidin Channel Interior,

Transport Through Membranes: Carriers, Channels and Pumps,

A. Pullman et al., editors, 187-201 (Kluwer Academic Publishers, 1988),

by D. Busath, G. Hemsley, T. Bridal, M. Pear, K. Gaffney, and M. Karplus.

 

365.  Molecular Dynamics Simulation of the Primary Processes in the Photosynthetic Reaction

Center of Rhodopseudomonas Viridis,

Transport Through Membranes: Carriers, Channels and Pumps,

A. Pullman et al., editors, 513-525 (Kluwer Academic Publishers, 1988),

by H. Treutlein, C. Niedermeier, K. Schulten, J. Deisenhofer, H. Michel, A. T. Br¸nger, and M. Karplus.

 

366.  Protein Secondary Structure Prediction with a Neural Network,

Proc. Natl. Acad. Sci. USA 86, 152-156 (1989),

by L. H. Holley and M. Karplus.

 

367.  Simulations of Proteins,

Highlights of Modern Biochemistry, A. Kotyk, J. Skoda, V. Paces, and V. Kostka, editors, 3-10

(VSP International Science Publishers, Zeist, Czechoslovakia, 1989),

by M. Karplus, R. Elber, J. Gao, K. Kuczera, and B. Tidor.

 

368.  Dynamics and Thermodynamics of Myoglobin and Hemoglobin,

Cytochrome P-450: Biochemistry and Biophysics, Proceedings of the 6th Internat'l Congress,

I. Schuster, editor, 258-265 (Taylor & Francis Inc., Philadelphia, 1989),

by M. Karplus, R. Elber, J. Gao, K. Kuczera, and B. Tidor.

 

369.  Crystallographic Refinement by Simulated Annealing: Application to Crambin,

Acta Cryst. A45, 50-61 (1989),

by A. T. Br¸nger, M. Karplus, and G. A. Petsko.

 

370.  Internal Dynamics of Globular Proteins: Comparison of Neutron Scattering Measurements and

Theoretical Models,

Physica B156 & 157, 437-443 (1989),

by J. Smith, K. Kuczera, B. Tidor, W. Doster, S. Cusack, and M. Karplus.

 

371.  Molecular & Harmonic Dynamics Simulations of Proteins,

Science at the John von Neumann Nat'l Supercomputer Center:  Annual Research Report FY 1988,

117-125 (1989),

by C. Lim, D. Nguyen, J. Straub, B. Tidor, and M. Karplus.

 

372.  Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis,

Science 244, 1069-1072 (1989),

by J. Gao, K. Kuczera, B. Tidor, and M. Karplus.

 

373.  Solvent Effects on Protein Motion and Protein Effects on Solvent Motion: Dynamics of the

Active Site Region of Lysozyme,

J. Mol. Biol. 208, 159-181 (1989),

by C. L. Brooks III and M. Karplus.

 

374.  A Molecular Dynamics Analysis of Protein Structural Elements,

Proteins 5, 337-354 (1989),

by C. B. Post, C. M. Dobson, and M. Karplus.

 

375.  Inertial Effects in Butane Stochastic Dynamics,

J. Chem. Phys. 91, 211-218 (1989),

by R. W. Pastor and M. Karplus.

 

376.  Structure & Function of Hemoglobin: The Cooperative Mechanism,

Allosteric Enzymes, G. HervÈ, editor, 27-59 (CRC Press, 1989),

by M. Karplus, D. A. Case, B. Gelin, B. H. Huynh, A. W.-M. Lee, and A. Szabo.

 

377.  Basis Set and Polarization Function Effects on Optimized Geometries and Harmonic Frequencies

at the Second-Order Moller-Plesset Perturbation Level,

J. Chem. Phys. 91, 1719-1733 (1989),

by H. Guo and M. Karplus.

 

378.  X-ray Refinement of Protein Structures by Simulated Annealing: Test of the Method on Myohemerythrin,

Acta Cryst. A45, 396-409 (1989),

by J. Kuriyan, A. T. Br¸nger, M. Karplus, and W. A. Hendrickson.

 

379.  Two-Dimensional NMR and Photo-CIDNP Studies of the Insulin Monomer: Assignment of

Aromatic Resonances with Application to Protein Folding, Structure, and Dynamics,

Biochemistry 28, 9855-9873 (1989),

by M. A. Weiss, D. T. Nguyen, I. Khait, K. Inouye, B. H. Frank, M. Beckage, E. O'Shea,

S. E. Shoelson, M. Karplus, and L. J. Neuringer.

 

380.  Molecular Dynamics: Applications to Proteins,

Protein Structure and Engineering, Life Sciences 183,

O. Jardetsky, editor, 269-290 (Plenum Press, New York, 1989),

by M. Karplus.

 

381.  Construction of Sidechains in Homology Modelling. Application to the C-Terminal Lobe of

Rhizopuspepsin,

J. Mol. Biol. 210, 785-812 (1990),

by N. L. Summers and M. Karplus.

 

382.  Dynamics of Myoglobin: Comparison of Simulation Results with Neutron Scattering Spectra,

Proc. Natl. Acad. Sci. USA 87, 1601-1605 (1990),

by J. Smith, K. Kuczera, and M. Karplus.

 

383.  Solvation Thermodynamics: An Approach from Analytic Temperature Derivatives,

J. Chem. Phys. 92, 5020-5033 (1990),

by H.-A. Yu, B. Roux, and M. Karplus.

 

384.  Simulation Analysis of Structures on the Reaction Pathway of RNAase A,

J. Am. Chem. Soc. 112, 3826-3831 (1990),

by K. Haydock, C. Lim, A. Br¸nger, and M. Karplus.

 

385.  Lysozyme Hydrolysis of b-Glycosides: A Consensus Between Binding Interactions and Mechanisms,

ACS Symposium Series 430, J. Brady and A. French, editors, Chapter 23, 377-388 (1990),

by C. B. Post, C. M. Dobson, and M. Karplus.

 

386.  Temperature Dependence of the Structure and Dynamics of Myoglobin: A Simulation Approach,

J. Mol. Biol. 213, 351-373 (1990),

by K. Kuczera, J. Kuriyan and M. Karplus.

 

387.  Molecular Basis for the Born Model of Ion Solvation,

J. Phys. Chem. 94, 4683-4688 (1990),

by B. Roux, H.-A. Yu, and M. Karplus.

 

388.  Motions of an a Helical Polypeptide: Comparison of Molecular and Harmonic Dynamics,

Biopolymer 29, 645-677 (1990),

by D. Perahia, R. M. Levy, and M. Karplus.

 

389.  A Combined Quantum Mechanical and Molecular Mechanical Potential for

Molecular Dynamics Simulations,

J. Comp. Chem. 11, 700-733 (1990),

by M. J. Field, P. A. Bash, and M. Karplus.

 

390.  A Theoretical Investigation of the AlC2H4 Complex,

Chem. Phys. Lett. 169, 410-415 (1990),

by J. Gao and M. Karplus.

 

391.  Three-Dimensional "Pople Diagram",

J. Phys. Chem. 94, 5435-5436 (1990),

by M. Karplus.

 

392.  The Diffusion-Collision Model of Protein Folding, in

Protein Folding: Deciphering the Second Half of the Genetic Code, L. M. Gierasch and J. King, editors, 283-290 (American Association for the Advancement of Science, Washington, D.C., 1990),

by D. Bashford, M. Karplus, and D. L. Weaver.

 

393.  Ab Initio Study of the Vibrational Spectra of N9-H and N7-H Adenine and 9-Methyladenine,

J. Am. Chem. Soc. 112, 5324-5340 (1990),

by J. WiÛrkiewicz-Kuczera and M. Karplus.

 

394.  An Integral Equation Theory Study of the Solvent-Induced Reaction Barrier in the

Nucleophilic Addition of Hydroxide to Formaldehyde,

J. Am. Chem. Soc. 112, 5706-5716 (1990),

by H.-A. Yu and M. Karplus.

 

395.  Nonexistence of Dianionic Pentacovalent Intermediates in the Ab Initio Study of the Base-Catalyzed

Hydrolysis of Ethylene Phosphate,

J. Am. Chem. Soc. 112, 5872-5873 (1990),

by C. Lim and M. Karplus.

 

396.  Inelastic Neutron Scattering Analysis of Low Frequency Motions in Proteins: Harmonic and

Damped Harmonic Models of Bovine Pancreatic Trypsin Inhibitor,

J. Chem. Phys. 93, 2974-2991 (1990),

by J. Smith, S. Cusack, B. Tidor, and M. Karplus.

 

397.  The Interpretation of Site-Directed Mutagenesis Experiments by Linear Free Energy Relations,

Protein Engineering 3, 673-675 (1990),

by J. Straub and M. Karplus.

 

398.  Modeling of Globular Proteins: A Distance-Based Data Search Procedure for the Construction of

Insertion/Deletion Regions and Pro ´ nonPro Mutations,

J. Mol. Biol. 216, 991-1016 (1990),

by N. L. Summers and M. Karplus.

 

399.  Conformational Sampling Using High Temperature Molecular Dynamics,

Biopolymers 29, 1847-1862 (1990),

by R. E. Bruccoleri and M. Karplus.

 

400.  Conserved Sequence and Structural Elements in the HIV-1 Principal Neutralizing Determinant,

Science 249, 932-935 (1990),

by G. J. LaRosa, J. P. Davide, K. Weinhold, J. A. Waterbury, A. T. Profy, J. A. Lewis,

A. J. Langlois, G. R. Dreesman, R. N. Boswell, P. Shadduck, L. H. Holley, M. Karplus,

D. P. Bolognesi, T. J. Matthews, E. A. Emini, and S. D. Putney.

 

401.  Anatomy of a Protein Conformational Change: Hinged "Lid" Motion of the

Triosephosphate Isomerase Loop,

Science 249, 1425-1428 (1990),

by D. Joseph, G. A. Petsko, and M. Karplus.

 

402.  The pKa's of Ionizable Groups in Proteins: Atomic Details From a Continuum Electrostatic Model,

Biochemistry 29, 10219-10225 (1990),

by D. Bashford and M. Karplus.

 

403.  Free Energy of Sickling: A Simulation Analysis,

Proc. Natl. Acad. Sci. USA 87, 8481-8485 (1990),

by K. Kuczera, J. Gao, B. Tidor and M. Karplus.

 

404.  Molecular Dynamics Simulations in Biology,

Nature 347, 631-639 (1990),

by M. Karplus and G. A. Petsko.

 

405.  Multidimensional Variational Gaussian Wave Packet Dynamics with Application to

Photodissociation Spectroscopy,

J. Chem. Phys. 93, 3919-3930 (1990),

by R. D. Coalson and M. Karplus.

 

406.  Electronic Structure of Icosahedral Cobalt-Sulfur Clusters,

J. Am. Chem. Soc. 112, 8705-8714 (1990),

by G. G. Hoffman, J. K. Bashkin, and M. Karplus.

 

407.  Enhanced Sampling in Molecular Dynamics: Use of the Time-Dependent Hartree Approximation for

a Simulation of Carbon Monoxide Diffusion through Myoglobin,

J. Am. Chem. Soc. 112, 9161-9175 (1990),

by R. Elber and M. Karplus.

 

408.  Molecular Dynamics: Applications to Proteins,

Modelling of Molecular Structures and Properties. Proceedings of an International Meeting,

Nancy, France, 1989, J.-L. Rivail, editor, 427-461 (Elsevier Science Publishers, Amsterdam, 1990),

by M. Karplus.

 

409.  Solvent Effect on the Anomeric Equilibrium in D-glucose: A Free Energy Simulation Analysis,

J. Am. Chem. Soc. 113, 1553-1557 (1991),

by S. Ha, J. Gao, B. Tidor, J. Brady, and M. Karplus.

 

410.  Model for the Structure of the Lipid Bilayer,

Proc. Natl. Acad. Sci. USA 88, 892-896 (1991),

by R. W. Pastor, R. M. Venable, and M. Karplus.

 

411.  Molecular Dynamics Simulations with Experimental Restraints,

Acc. Chem. Res. 24, 54-61 (1991),

by A. T. Br¸nger and M. Karplus.

 

412.  Ab initio Studies of Polyenes (I) 1,3-butadiene,

J. Chem. Phys. 94, 3679-3699 (1991),

by H. Guo and M. Karplus.

 

413.  FK506 and Rapamycin Binding to FKBP: Common Elements in Immunophilin-Ligand Complexation,

J. Am. Chem. Soc. 113, 2339-2341 (1991),

by T. J. Wandless, S. W. Michnick, M. K. Rosen, M. Karplus, and S. L. Schreiber.

 

414.  Aqueous Solvation of N-Methylacetamide Conformers: Comparison of Simulations and Integral

Equation Theories,

J. Am. Chem. Soc. 113, 2425-2434 (1991),

by H.-A. Yu, M. Karplus, and B. M. Pettitt.

 

415.  Simulation Analysis of the Stability Mutant R96H of T4 Lysozyme,

Biochemistry 30, 3217-3228 (1991),

by B. Tidor and M. Karplus.

 

416.  Ion Transport in a Gramicidin Channel: Structure and Thermodynamics,

Biophys. J. 59, 961-981 (1991),

by B. Roux and M. Karplus.

 

417.  Energy Equipartitioning in the Classical Time-Dependent Hartree Approximation,

J. Chem. Phys. 94, 6737-6739 (1991),

by J. E. Straub and M. Karplus.

 

418.  Demonstration by NMR of Folding Domains in Lysozyme,

Nature 349, 633-636 (1991),

by A. Miranker, S. E. Radford, M. Karplus, and C. M. Dobson.

 

419.  Ligand Binding and Protein Relaxation in Heme Proteins: A Room  Temperature Analysis

of NO Geminate Recombination,

Biochemistry 30, 3975-3987 (1991),

by J. W. Petrich, J.-C. Lambry, K. Kuczera, M. Karplus, C. Poyart, and J.-L. Martin.

 

420.  Proton and Nitrogen Sequential Assignments and Secondary Structure Determination of the Human

FK506 and Rapamycin Binding Protein,

Biochemistry 30, 4774-4789 (1991),

by M. K. Rosen, S. W. Michnick, M. Karplus, and S. L. Schreiber.

 

421.  Dianionic Pentacoordinate Species in the Base-Catalyzed Hydrolysis of Ethylene and

Dimethyl Phosphate,

J. Am. Chem. Soc. 113, 4353-4355 (1991),

by A. Dejaegere, C. Lim, and M. Karplus.

 

422.  Exploration of Disorder in Protein Structures by X-Ray Restrained Molecular Dynamics,

Proteins: Structure, Function & Genetics 10, 340-358 (1991),

by J. Kuriyan, K. Osapay, S. K. Burley, A. T. Br¸nger, W. A. Hendrickson, and M. Karplus.

 

423.  Ion Transport in a Gramicidin-like Channel: Dynamics and Mobility,

J. Phys. Chem. 95, 4856-4868 (1991),

by B. Roux and M. Karplus.

 

424.  Absolute pKa Calculations with Continuum Dielectric Methods,

J. Phys. Chem. 95, 5610-5620 (1991),

by C. Lim, D. Bashford, and M. Karplus.

 

425.  Structure of the Triosephosphate Isomerase-Phosphoglycolohydroxamate Complex:

An Analog of the Intermediate on the Reaction Pathway,

Biochemistry 30, 5821-5826 (1991),

by R. C. Davenport, P. A. Bash, B. A. Seaton, M. Karplus, G. A. Petsko, and D. Ringe.

 

426.  Computer Simulation and Analysis of the Reaction Pathway of Triosephosphate Isomerase,

Biochemistry 30, 5826-5832 (1991),

by P. A. Bash, M. J. Field, R. C. Davenport, G. A. Petsko, D. Ringe, and M. Karplus.

 

427.  Prediction of Optimal Peptide Mixtures to Induce Broadly Neutralizing Antibodies to

Human Immunodeficiency Virus Type 1,

Proc. Natl. Acad. Sci. USA 88, 6800-6804 (1991),

by L. H. Holley, J. Goudsmit, and M. Karplus.

 

428.  Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method,

Proteins: Structure, Function & Genetics 11, 29-34 (1991),

by A. Miranker and M. Karplus.

 

429.  Solution Structure of FKBP, a Rotamase Enzyme and Receptor for FK506 and Rapamycin,

Science 252, 836-839 (1991),

by S. W. Michnick, M. K. Rosen, T. J. Wandless, M. Karplus, and S. L. Schreiber.

 

430.  Protein Folding Bottlenecks: A Lattice Monte Carlo Simulation,

Phys. Rev. Lett. 67, 1665-1668 (1991),

by E. Shakhnovich, G. Farztdinov, A. M. Gutin, and M. Karplus.

 

431.  Modeling of Side Chains, Loops and Insertions in Proteins,

Methods in Enzymology 202, J. J. Lagone, editor, 156-204 (Academic Press, Inc., 1991),

by N. L. Summers and M. Karplus. 

 

432.  Neural Networks for Protein Structure Prediction,

Methods in Enzymology 202, J. J. Lagone, editor, 204-224 (Academic Press, Inc., 1991),

by L. H. Holley and M. Karplus. 

 

433.  Molecular Dynamics of Carbon Monoxide After Photodissociation from Myoglobin,

AIP Conference Proceedings 239, Advances in Biomolecular Simulations: Obernai, France 1991,

R. Lavery, J.-L. Rivail, and J. Smith, editors, 147-152 (American Institute of Physics, 1991),

by J. E. Straub and M. Karplus.

 

434.  Analysis of the Stability Mutant Ile 96 Æ Ala in Barnase, Based on Free Energy Simulations,

AIP Conference Proceedings 239, Advances in Biomolecular Simulations: Obernai, France 1991,

R. Lavery, J.-L. Rivail, and J. Smith, editors 283-292 (American Institute of Physics, 1991),

by S. J. Wodak, M. PrÈvost, B. Tidor, and M. Karplus.

 

435.  Simulation Analysis of the Stability Mutants R96H of Bacteriophage T4 Lysozyme and I96A of Barnase,

Protein Conformation, Ciba Foundation Symposium 161, 63-74 (John Wiley & Sons, 1991),

by M. Karplus, M. PrÈvost, B. Tidor and S. Wodak.

 

436.  Collective Motions in Proteins: A Covariance Analysis of Atomic Fluctuations in Molecular Dynamics

and Normal Mode Simulations,

Proteins: Structure, Function & Genetics 11, 205-217 (1991),

by T. Ichiye and M. Karplus.

 

437.  Multiple-Site Titration Curves of Proteins: An Analysis of Exact and Approximate Methods for

Their Calculation,

J. Phys. Chem. 95, 9556-9561 (1991),

by D. Bashford and M. Karplus.

 

438.  Importance of Attractive van der Waals Contribution in Empirical Energy Function Models for the

Heat of Vaporization of Polar Liquids,

J. Phys. Chem. 95, 10559-10560 (1991),

by A. D. MacKerell, Jr. and M. Karplus.

 

439.  Molecular Dynamics Study of the Photodissociation of Carbon Monoxide from Myoglobin:

Ligand Dynamics in the First 10 ps,

Chemical Physics 158, 221-248 (1991),

by J. Straub and M. Karplus.

 

440.  Contribution of the Hydrophobic Effect to Protein Stability: Analysis Based on Simulations of the

Ile 96 Æ Ala Mutation in Barnase,

Proc. Natl. Acad. Sci. USA 88, 10880-10884 (1991),

by M. PrÈvost, S. J. Wodak, B. Tidor, and M. Karplus.

 

441.  On the Treatment of Electrostatic Interactions in Biomolecular Simulation,

J. Chim. Phys. 88, 2419-2433 (1991),

by R. H. Stote, D. J. States, and M. Karplus.

 

442.  Torsional Motions of Methyl and Ammonium Groups in the L-alanine Crystal:

A Comparison of Molecular Dynamics and Normal Mode Calculations,

J. Chim. Phys. 88, 2587-2596 (1991),

by J. Garen, M. J. Field, G. Kneller, M. Karplus, and J. Smith.

 

443.  Dynamical Search for bis-penicillamine enkephalin Conformations,

Biophys. J. 60, 1540-1544 (1991),

by B. M. Pettitt, T. Matsunaga, F. Al-Obeidi, C. Gehrig, V. J. Hruby, and M. Karplus.

 

444.  Simulation Analysis of Triose Phosphate Isomerase: Conformation Transition and Catalysis,

Faraday Discussions 93, 239-248 (1992),

by M. Karplus, J. D. Evanseck, D. Joseph, P. A. Bash, and M. J. Field.

 

445.  Empirical Force Field Study of Geometries and Conformational Transitions of Some Organic

Molecules,

J. Am. Chem. Soc. 114, 801-812 (1992),

by J. C. Smith and M. Karplus.

 

446.  Chromophore-Protein Interactions and the Function of the Photosynthetic Reaction Center:

A Molecular Dynamics Study,

Proc. Natl. Acad. Sci. USA 89, 75-79 (1992),

by H. Treutlein, K. Schulten, A. Br¸nger, M. Karplus, J. Deisenhofer, and H. Michel.

 

447.  Effective Coupling in Bridged Electron Transfer Molecules: Computational Formulation and Examples,

J. Chem. Phys. 96, 5272-5278 (1992),

by J. Evenson and M. Karplus.

 

448.  fl-Sheet Coil Transitions in a Simple Polypeptide Model,

Proteins: Structure, Function & Genetics 12, 237-265 (1992),

by K. Yapa, D. L. Weaver, and M. Karplus.

 

449.  Conjugate Peak Refinement: An Algorithm for Finding Reaction Paths and Accurate Transition-States

in Systems with Many Degrees of Freedom,

Chem. Phys. Lett. 194, 252-261 (1992),

by S. Fischer and M. Karplus.

 

450.  Ab Initio Studies of Hydrogen Bonding of N-Methylacetamide: Structure, Cooperativity, and

Internal Rotational Barriers,

J. Phys. Chem. 96, 7273-7287 (1992),

by H. Guo and M. Karplus.

 

451.  Ab Initio Studies of Methylated 1,3-Butadienes,

J. Molecular Structure (Theochem) 260, 347-393 (1992),

by H. Guo and M. Karplus.

 

452.  Protein Folding: Theoretical Studies of Thermodynamics and Dynamics,

Protein Folding, T. E. Creighton, editor, Chapter 4, 127-195 (W.H. Freeman & Sons, 1992),

by M. Karplus and E. Shakhnovich.

 

453.  Molecular Modelling of Protein - Ligand Interactions,

Bull. Soc. Chim. Belg. 101, 661-662 (1992),

by P.D.J. Grootenhuis, V. J. van Geerestein, C.A.G. Haasnoot, and M. Karplus.

 

454.  The Influence of Rapid Intramolecular Motion on NMR Cross-Relaxation Rates.

A Molecular Dynamics Study of Antamanide in Solution,

J. Am. Chem. Soc. 114, 2289-2302 (1992),

by R. Br¸schweiler, B. Roux, M. Blackledge, C. Griesinger, M. Karplus, and R. R. Ernst.

 

455.  The Contribution to Cross-Links to Protein Stability: A Normal Mode Analysis of the

Configurational Entropy of the Native State,

Proteins: Structure, Function & Genetics 15, 71-79 (1993),

by B. Tidor and M. Karplus.

 

456.  Backbone Dependent Rotamer Library for Proteins: Application to Side-chain Prediction,

J. Mol. Biol. 230, 543-574 (1993),

by R. L. Dunbrack, Jr. and M. Karplus.

 

457.  Ion Transport in the Gramicidin Channel:  Free Energy of the Solvated Right-handed Dimer in a

Model Membrane,

J. Am. Chem. Soc. 115, 3250-3262 (1993),

by B. Roux and M. Karplus.

 

458.  Three-Dimensional Models of Four Mouse Mast Cell Chymases. Identification of Proteoglycan

Binding Regions and Protease-Specific Antigenic Epitopes,

J. Biol. Chem. 268, 9023-9034 (1993),

by A. Sali, R. Matsumoto, H. P. McNeil, M. Karplus, and R. L. Stevens.

 

459.  Hydrolysis Rate Difference between Cyclic and Acyclic Phosphate Esters: Solvation versus Strain,

J. Am. Chem. Soc. 115, 5316-5317 (1993),

by A. Dejaegere and M. Karplus.

 

460.  Temperature Echoes in Molecular Dynamics Simulations of Proteins,

Phys. Rev. Letts. 70, 3514-3517 (1993),

by O. M. Becker and M. Karplus.

 

461.  Multiple Copy Simultaneous Search and Construction of Ligands in Binding Sites: Application to

Inhibitors of HIV-1 Aspartic Proteinase,

J. Med. Chem. 36, 2142-2167 (1993),

by A. Caflisch, A. Miranker, and M. Karplus.

 

462.  Stochastic Dynamics Simulations of the Alanine Dipeptide Using a Solvent-Modified Potential

Energy Surface,

J. Phys. Chem. 97, 6907-6913 (1993),

by P. E. Smith, B. M. Pettitt and M. Karplus.

 

463.  The Nature of the Ion Binding Interactions in EF-Hand Peptide Analogs: Free Energy Simulation

of Asp to Asn Mutations,

Protein Engineering 6, 585-592 (1993),

by B. Prod'hom and M. Karplus.

 

464.  Nonexponential Relaxation after Ligand Dissociation from Myoglobin:

A Molecular Dynamics Simulation,

Proc. Natl. Acad. Sci. USA 90, 5805-5807 (1993),

by K. Kuczera, J.-C. Lambry, J.-L. Martin, and M. Karplus.

 

465.  Active Site Dynamics of Acyl-Chymotrypsin,

Proteins: Structure, Function & Genetics 16, 172-194 (1993),

by S. Nakagawa, H.-A. Yu, M. Karplus, and H. Umeyama.

 

466.  Molecular Dynamics Simulations of Disulfide Cross-Linked DNA Decamers,

J. Am. Chem. Soc. 115, 7569-7583 (1993),

by A. E. Ferentz, J. WiÛrkiewicz-Kuczera, M. Karplus, and G. L. Verdine.

 

467.  Molecular Dynamics Simulation of the Proline Conformational Equilibrium and Dynamics in

Antamanide Using the CHARMM Force Field,

J. Am. Chem. Soc. 115, 8747-8756 (1993),

by J. M. Schmidt, R. Br¸schweiler, R. R. Ernst, R. L. Dunbrack, Jr., D. Joseph, and M. Karplus.

 

468.  Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods,

J. Chem. Phys. 99, 8063-8074 (1993),

by M. Watanabe and M. Karplus.

 

469.  Effective Coupling in Biological Electron Transfer: Exponential or Complex Distance Dependence?,

Science 262, 1247-1249 (1993),

by J. Evenson and M. Karplus.

 

470.  Internal Motions of Proteins,

Ultrafast Phenomena VIII, J.-L. Martin, A. Migus, G. A. Mourou, and A. H. Zewail, editors,

Springer Series in Chemical Physics 55, 13-14 (1993),

by M. Karplus.

 

471.  Preface,

Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Vol. 2,

W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors, v-xix (Kluwer Academic Publishers, 1994),

by M. Karplus.

 

472.  A Mechanism for Rotamase Catalysis by the FK506 Binding Protein (FKBP),

Biochemistry  32, 13830-13837 (1994),

by S. Fischer, S. Michnick, and M. Karplus.

 

473.  Kinetics of Protein Folding: A Lattice Model Study of the Requirements for Folding to the

Native State,

J. Mol. Biol. 235, 1614-1636 (1994),

by A. Sali, E. Shakhnovich, and M. Karplus.

 

474.  Molecular Recognition in Proteins: Simulation Analysis of Substrate Binding by Tyrosyl-tRNA

Synthetase Mutants,

J. Mol. Biol. 236, 1049-1066 (1994),

by F.T.K. Lau and M. Karplus.

 

475.  Simulation Analysis of the Binding Interactions in the RNase A/3¥-UMP Enzyme-Product Complex

as a Function of pH,

J. Am. Chem. Soc. 116, 2591-2599 (1994),

by J. E. Straub, C. Lim, and M. Karplus.

 

476.  Molecular Dynamics Simulation of Protein Denaturation: Solvation of the Hydrophobic Cores

and Secondary Structure of Barnase,

Proc. Natl. Acad. Sci. USA 91, 1746-1750 (1994),

by A. Caflisch and M. Karplus.

 

477.  Protein Folding Dynamics: The Diffusion-Collision Model and Experimental Data,

Protein Science 3, 650-668 (1994),

by M. Karplus and D. L. Weaver.

 

478.  Conformational Analysis of the Backbone-Dependent Rotamer Preferences of Protein Sidechains,

Nature Struct. Biol. 1, 334-340 (1994),

by R. L. Dunbrack, Jr. and M. Karplus.

 

479.  Molecular Dynamics Simulations of the Gramicidin Channel,

Annu. Rev. Biophys. Biomol. Struct. 23, 731-761 (1994),

by B. Roux and M. Karplus.

 

480.  The Contribution of Vibrational Entropy to Molecular Association: The Dimerization of Insulin,

J. Mol. Biol. 238, 405-414 (1994),

by B. Tidor and M. Karplus.

 

481.  Analysis of Two-Residue Turns in Proteins,

J. Mol. Biol. 238, 733-747 (1994),

by C. Mattos, G. A. Petsko, and M. Karplus.

 

482.  How Does a Protein Fold?

Nature 369, 248-251 (1994),

by A. Sali, E. Shakhnovich, and M. Karplus.

 

483.  Molecular Dynamics Studies of Protein and Peptide Folding and Unfolding,

The Protein Folding Problem and Tertiary Structure Prediction, K. Merz, Jr. and S. Le Grand,

editors, Chapter 7, 195-232 (Birkh‰user, Boston, MA, 1994),

by A. Caflisch and M. Karplus.

 

484.  Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox,

The Protein Folding Problem and Tertiary Structure Prediction, K. Merz, Jr. and S. Le Grand,

editors, Chapter 14, 435-508 (Birkh‰user, Boston, MA, 1994),

by J. T. Ngo, J. Marks, and M. Karplus.

 

485.  Molecular Recognition: An Example from Ligand Binding to Proteins,

Computational Approaches in Supramolecular Chemistry 426, G. Wipff, editor, 477-494

(Kluwer Academic Publishers, 1994),

by M. Karplus and F.T.K. Lau.

 

486.  Phosphate Ester Hydrolysis: Calculation of Gas-phase Reaction Paths and Solvation Effects,

J. Chem. Soc. Faraday Trans. 90, 1763-1770 (1994),

by A. Dejaegere, X. Liang, and M. Karplus.

 

487.  Phase Diagram of a Model Protein Derived by Exhaustive Enumeration of the Conformations,

J. Chem. Phys. 101, 1444-1451 (1994),

by A. R. Dinner, A. Sali, M. Karplus, and E. Shakhnovich.

 

488.  HOOK: A Program for Finding Novel Molecular Architectures that Satisfy the Chemical and

Steric Requirements of a Macromolecule Binding Site,

Proteins: Structure, Function & Genetics 19, 199-221 (1994),

by M. B. Eisen, D. C. Wiley, M. Karplus, and R. E. Hubbard.

 

489.  Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis,

Israel J. Chem. 34, 233-238 (1994),

by F. Nardi, W. Doster, B. Tidor, M. Karplus, S. Cusack, and J. C. Smith.

 

490.  Solvent Influence on the Stability of the Peptide Hydrogen Bond: A Supramolecular Cooperative Effect,

J. Phys. Chem. 98, 7104-7105 (1994),

by H. Guo and M. Karplus.

 

491.  Free Energy Simulations: The Meaning of the Individual Contributions from a Component Analysis,

Proteins: Structure, Function & Genetics 20, 25-33 (1994),

by S. Boresch, G. Archontis, and M. Karplus.

 

492.  Cis-Trans Imide Isomerization of the Proline Dipeptide,

J. Am. Chem. Soc. 116, 11931-11937 (1994),

by S. Fischer, R. L. Dunbrack, Jr. and M. Karplus.

 

493.  Pathways for Conformational Interconversion of Calix[4]arenes,

J. Am. Chem. Soc. 117, 1611-1620 (1995),

by S. Fischer, P. D. J. Grootenhuis, L. C. Groenen, W. P. van Hoorn, F.C.J.M. van Veggel, D. N. Reinhoudt, and M. Karplus.

 

494.  Theoretical Studies of Protein Folding & Unfolding,

Current Opinion in Structural Biology 5, 58-73 (1995),

by M. Karplus and A. Sali.

 

495.  Protein Dynamics: From the Native to the Unfolded State and Back Again,

Modelling of Biomolecular Structures and Mechanisms, A. Pullman et al., editors, 69-84

(Kluwer Academic Publishers, 1995),

by M. Karplus, A. Caflisch, A. Sali, and E. Shakhnovich.

 

496.  Simulations of Macromolecules by Multiple Time-Step Methods,

J. Phys. Chem. 99, 5680-5697 (1995),

by M. Watanabe and M. Karplus.

 

497.  pH Dependence of Binding Reactions from Free Energy Simulations and Macroscopic Continuum

Electrostatic Calculations: Application to 2¥GMP / 3¥GMP Binding to Ribonuclease T1 and Implications for Catalysis,

J. Mol. Biol. 247, 774-807 (1995),

by A.D. MacKerell Jr., M.S. Sommer and M. Karplus.

 

498.  Neural Networks for Secondary Structure and Structural Class Predictions,

Protein Science 4, 275-285 (1995),

by J.-M. Chandonia and M. Karplus.

 

499.  Ion Transport in the Gramicidin Channel: Molecular Dynamics Study of Single and Double Occupancy,

Biophys. J. 68, 876-892 (1995),

by B. Roux, B. Prod'hom, and M. Karplus.

 

500.  Acid and Thermal Denaturation of Barnase Investigated by Molecular Dynamics Simulations,

J. Mol. Biol. 252, 672-708 (1995),

by A. Caflisch and M. Karplus.

 

501.  Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation,

Proteins: Structure, Function & Genetics 23, 12-31 (1995),

by R. H. Stote and M. Karplus.

 

502.  Enthalpic Contribution to Protein Stability: Atom-Based Calculations and Statistical Mechanics,

Adv. Protein Chem. 47, 231-306 (Academic Press, Inc. 1995),

by T. Lazaridis, G. Archontis, and M. Karplus.

 

503.  Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study,

J. Comp. Chem. 16, 690-704 (1995),

by B. Roux and M. Karplus.

 

504.  Packaging of Proteases and Proteoglycans in the Granules of Mast Cells and Other Hematopoietic Cells,

J. Biol. Chem. 270, 19524-19531 (1995),

by R. Matsumoto, A. Sali, N. Ghildyal, M. Karplus, and R. L. Stevens.

 

505.  Protein Folding Studied by Monte Carlo Simulations,

Protein Folds: A Distance-Based Approach, H. Bohr and S. Brunak, editors, 202-217

(CRC Press, 1995),

by A. Sali, E. Shakhnovich, and M. Karplus.

 

506.  An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids,

J. Am. Chem. Soc. 117, 11946-11975 (1995),

by A. D. MacKerell Jr., J. WiÛrkiewicz-Kuczera, and M. Karplus.

 

507.  Harmonic Analysis of Large Systems. I. Methodology,

J. Comp. Chem. 16, 1522-1542 (1995),

by B. R. Brooks, D. Janezic, and M. Karplus.

 

508.  The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific

Interactions,

J. Mol. Biol. 254, 801-807 (1995),

by S. Boresch and M. Karplus.

 

509.  Evaluation of Comparative Protein Modeling by MODELLER,

Proteins: Structure, Function & Genetics 23, 318-326 (1995),

by A. Sali, L. Pottertown, F. Yuan, H. van Vlijmen, and M. Karplus.

 

510.  Automated Method for Dynamic Ligand Design,

Proteins: Structure, Function & Genetics  23, 472-490 (1995),

by A. Miranker and M. Karplus.

 

511.  Temperature Quench Echoes in Proteins,

J. Chem. Phys. 103, 3112-3123 (1995),

by D. Xu, K. Schulten, O. Becker and M. Karplus.

 

512.  Computational Combinatorial Chemistry for de novo Ligand Design: Review and Assessment,

Perspectives in Drug Discovery & Design 3: De Novo Design, K. M¸ller, editor, 51-84

(ESCOM, Leiden, 1995),

by A. Caflisch and M. Karplus.

 

513.  Use of a Minimum Perturbation Approach to Predict TIM Mutant Structures,

Protein Engineering 8, 1103-1115 (1995),

by D. Joseph-McCarthy, G. Petsko, and M. Karplus.

 

514.  Protein Dynamics: From the Native to the Unfolded State and Back Again,

Proceedings of the International Conference on Molecular Structural Biology, A. J. Kungl,

P. J. Andrew, and H. Schreiber, editors, 129-155 (Gesellschaft ÷sterreichischer Chemiker, 1995),

by M. Karplus.

 

515.  A Comprehensive Analytical Treatment of Continuum Electrostatics,

J. Phys. Chem. 100, 1578-1599 (1996),

by M. Schaefer and M. Karplus.

 

516.  The Anomeric Equilibrium in D-Xylose: Free Energy and the Role of Solvent Structuring,

J. Am. Chem. Soc. 118, 541-546 (1996),

by R. K. Schmidt, M. Karplus, and J. W. Brady.

 

517.  Functionality Map Analysis of the Active Site Cleft of Human Thombin,

J. Computer-Aided Molecular Design. 10, 1-10 (1996),

by P.D.J. Grootenhuis and M. Karplus.

 

518.  Thermodynamics and Kinetics of Protein Folding,

Discrete Mathematics and Theoretical Computer Science 23, 199-213 (1996),

by A. Sali, E. Shakhnovich, and M. Karplus.

 

519.  Simulations of Enzymic Reactions,

Biochemistry Society Transactions 24, 247-254 (1996),

by A. J. Mulholland and M. Karplus.

 

520.  The Importance of Larger Data Sets for Protein Secondary Structure Prediction with Neural Networks,

Protein Science 5, 768-774 (1996),

by J.-M. Chandonia and M. Karplus.

 

521.  Evolutionary Optimization of QSAR: An Application of Genetic Neural Networks,

J. Med. Chem. 39, 1521-1530 (1996),

by S.-S. So and M. Karplus.

 

522.  New Formulation for the Derivatives of the Torsion Angles and Improper Torsion Angles in

Molecular Mechanics: Elimination of Singularities,

J. Comp. Chem. 17, 1132-1141 (1996),

by A. Blondel and M. Karplus.

 

523.  Analysis of Coupling Schemes in Free Energy Simulations: A Unified Description of Nonbonded

Contributions to Solvation Free Energies,

J. Phys. Chem. 26, 11148-11164 (1996),

by A. Dejaegere and M. Karplus.

 

524.  An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and

Applications,

Biological Membranes: A Molecular Perspective from Computation and Experiment,

K. M. Merz, Jr. and B. Roux, editors, 31-81 (Birkh‚user, 1996),

by M. Schlenkrich, J. Brickmann, A. D. MacKerell Jr., and M. Karplus.

 

525.  The Folding Mechanism of Larger Model Proteins: Role of Native Structure,

Proc. Natl. Acad. Sci. USA 93, 8356-8361 (1996),

by A. R. Dinner, A. Sali, and M. Karplus.

 

526.  Simulation of Activation Free Energies in Molecular Systems,

J. Chem. Phys. 105, 1902-1921 (1996),

by E. Neria, S. Fischer, and M. Karplus.

 

527.  Comment on a "Fluctuation and Cross Correlation Analysis of Protein Motions Observed in

Nanosecond Molecular Dynamics Simulations",

J. Mol. Biol. 263, 120-122 (1996),

by M. Karplus and T. Ichiye.

 

528.  Orientational Correlations and Entropy in Liquid Water,

J. Chem. Phys. 105, 4294-4316 (1996),

by T. Lazaridis and M. Karplus.

 

529.  The Jacobian Factor in Free Energy Simulations,

J. Chem. Phys. 105, 5145-5154 (1996),

by S. Boresch and M. Karplus.

 

530.  Genetic Neural Networks for Quantitative Structure-Activity Relationships: Improvements and

Application of Benzodiazepines Affinity for BZ/GABAA Receptors,

J. Med. Chem. 39, 5246-5256 (1996),

by S.-S. So and M. Karplus.

 

531.  A Position Dependent Friction Model for Solution Reactions in the High Friction Regime: Proton

Transfer in Triosephosphate Isomerase (TIM),

J. Chem. Phys. 105, 10812-10818 (1996),

by E. Neria and M. Karplus.

 

532.  Cumulant Expansion of the Free Energy: Application to Free Energy Derivatives and Component

Analysis,

J. Chem. Phys. 105, 11246-11260 (1996),

by G. Archontis and M. Karplus.

 

533.  Simulations of Lysozyme: Internal Motions and the Reaction Mechanism,

Lysozymes: Model Enzymes  in Biochemistry and Biology, P. JollËs, editor, 111-141

(Birkh‰user Verlag, Basel, 1996),

by M. Karplus and C. B. Post.

 

534.  A First-Order Disorder-to-Order Transition in an Isolated Homopolymer Model,

Phys. Rev. Lett. 77, 2822-2825 (1996),

by Y. Zhou, C. K. Hall and M. Karplus.

 

535.  Exact Results for the Effect of Bond Flexibility on the Structure and the Collapse Transition of

Isolated Square-Well Trimers,

J. Mol. Phys. 89, 1707-1717 (1996),

by Y. Zhou and M. Karplus.

 

536.  Theory of Vicinal Coupling Constants,

Encyclopedia of Nuclear Magnetic Resonance, Vol. 1: Historical Perspectives,

D. M. Grant and R. K. Harris, editors, 420-422 (John Wiley & Sons, 1996),

by M. Karplus.

 

537.  The Topology of Multidimensional Potential Energy Surfaces: Theory and Application to Peptide

Structure and Kinetics,

J. Chem. Phys. 106, 1495-1517 (1997),

by O. M. Becker and M. Karplus.

 

538.  The pH-Dependence of Protein Stability: Absolute Electrostatic Free Energy Differences,

J. Phys. Chem. B 101, 1663-1683 (1997),

by M. Schaefer, M. Sommer, and M. Karplus.

 

539.  PDB-Based Protein Loop Prediction: Parameters for Selection and Methods for Optimization,

J. Mol. Biol. 267, 975-1001 (1997),

by H.W.T. van Vlijmen and M. Karplus.

 

540.  A Comparison between Molecular Dynamics and X-ray Results for Dissociated CO in Myoglobin,

Nature Struc. Biol. 4, 202-208 (1997),

by D. Vitkup, P. A. Petsko, and M. Karplus.

 

541.  Molecular Dynamics of an Enzyme Reaction: Proton Transfer in TIM,

Chem. Phys. Letters 267, 23-30 (1997),

by E. Neria and M. Karplus.

 

542.  Computer Simulations of the OmpF Porin from the Outer Membrane of Escherichia coli,

Biophys. J. 72, 2094-2102 (1997),

by M. Watanabe, J. Rosenbusch, T. Schirmer, and M. Karplus.

 

543.  Molecular Mechanics and Dynamics Simulations of Enzymes,

Computational Approaches to Enzymatic Reactivity , G. N·ray-SzabÛ and A. Warshel, editors, 153-198 (Kluwer Academic Publishers, 1997),

by R. H. Stote, A. Dejaegere, and M. Karplus.

 

544.  Docking by Monte Carlo-Minimization with a Solvation Correction: Application to an

FKBP-Substrate Complex,

J. Comp. Chem. 18, 723-743 (1997),

by A. Caflisch, S. Fischer, and M. Karplus.

 

545.  Multidimensional Adaptive Umbrella Sampling: Applications to Mainchain and Sidechain Peptide

Conformations,

J. Comp. Chem. 18, 1450-1462 (1997),

by C. Bartels and M. Karplus.

 

546.  Pseudosystematic Conformational Search. Application to Cycloheptadecane,

J. Am. Chem. Soc. 119, 5656-5667 (1997),

by J. T. Ngo and M. Karplus.

 

547.  The Levinthal Paradox: Yesterday and Today,

Folding & Design 2, 569-576 (1997),

by M. Karplus.

 

548.  Continuum Treatment of Long-Range Interactions in Free Energy Calculations. Application

to Protein-Ligand Binding,

J. Phys. Chem. B 101, 8349-8362 (1997),

by T. Simonson, G. Archontis, and M. Karplus.

 

549.  Ligand Induced Conformational Changes in ras p21: A Normal Mode and Energy

Minimization Analysis,

J. Mol. Biol. 274, 114-131 (1997),

by J. Ma and M. Karplus.

 

550.  Molecular Switch in Signal Transduction: Reaction Paths of the Conformational Changes in ras p21,

Proc. Natl. Acad. Sci. USA 94, 11905-11910 (1997),

by J. Ma and M. Karplus.

 

551.  Use of Multiple Copy Simultaneous Search (MCSS) Method to Design a New Class of

Picornavirus Capsid Binding Drugs,

Proteins: Structure, Function & Genetics 29, 32-58 (1997),

by D. Joseph-McCarthy, J. Hogle, and M. Karplus.

 

552.  Equilibrium Thermodynamics of Homopolymers and Clusters: Molecular Dynamics and Monte Carlo

Simulations of Systems with Square-Well Interactions,

J. Chem. Phys. 107, 10691-10708 (1997),

by Y. Zhou, M. Karplus, J. M. Wichert, and C. K. Hall.

 

553.  Folding Thermodynamics of a Model Three-Helix-Bundle Protein,

Proc. Natl. Acad. Sci. USA 94, 14429-14432 (1997),

by Y. Zhou and M. Karplus.

 

554.  "New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations,

Science 278, 1928-1931 (1997),

by T. Lazaridis and M. Karplus.

 

555.  Three Dimensional Quantitative Structure-Activity Relationships from Molecular Similarity Matrices

and Genetic Neural Networks. 1. Method and Validations,

J. Med. Chem. 40, 4347-4359 (1997),

by S.-S. So and M. Karplus.

 

556.  Three Dimensional Quantitative Structure-Activity Relationships from Molecular Similarity Matrices

and Genetic Neural Networks. 2. Applications,

J. Med. Chem. 40, 4360-4371 (1997),

by S.-S. So and M. Karplus.

 

557.  Dynamics and Unfolding Pathways of a Hyperthermophilic and a Mesophilic Rubredoxin,

Protein Science 6, 2589-2605 (1997),

by T. Lazaridis, I. Lee, and M. Karplus.

 

558. Protein Dynamics: From Femtoseconds to Milliseconds,

Nobel Symposium 101: Femtochemistry & Femtobiology , V. Sundtrˆm, editor, 386-422

(Imperial College Press, 1997),

by M. Karplus.

 

559.  Preface,

Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Vol. 3,

W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors, v-ix (Kluwer Academic Publishers, 1997),

by M. Karplus.

 

560.  Titration Calculations of Foot-and-Mouth Disease Virus Capsids and Their Stabilities as a

Function of pH,

J. Mol. Biol. 275, 295-308 (1998),

by H. van Vlijmen, S. Curry, M. Schaefer, and M. Karplus.

 

561.  Specific Amino Acid Recognition by Aspartyl-tRNA Synthetase Studied by Free Energy Simulations,

J. Mol. Biol. 275, 823-846 (1998),

by G. Archontis, T. Simonson, D. Moras, and M. Karplus.

 

562.  A Metastable State in Folding Simulations of a Protein Model,

Nature Struct. Biol. 5, 236-241 (1998),

by A. R. Dinner and M. Karplus.

 

563.  Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy,

J. Phys. Chem. B 102, 865-880 (1998),

by C. Bartels and M. Karplus.

 

564.  Locally Accessible Conformations of Proteins: Multiple Molecular Dynamics Simulations of Crambin,

Protein Science 7, 649-666 (1998),

by L.S.D. Caves, J. D. Evanseck and M. Karplus.

 

565.  Temperature Dependence of the Folding Rate in a Simple Protein Model: Search for

a "Glass" Transition,

J. Chem. Phys. 108, 6466-6483 (1998),

by A. Gutin, A. Sali, V. Abkevich, M. Karplus, and E. I. Shakhnovich.

 

566.  Protein Folding: A Perspective from Theory and Experiment,

Angew. Chem. Int. Ed. 37, 868-893 (1998),

by C. M. Dobson, A. Sali, and M. Karplus.

 

567.  All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins,

J. Phys. Chem. B 102, 3586-3616 (1998),

by A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau,

C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. WiÛrkiewicz-Kuczera, D. Yin, and M. Karplus. 

 

568.  Electrostatic Contributions to Molecular Free Energies in Solution,

Adv. Protein Chem. 51, 1-57 (Academic Press, Inc. 1998),

by M. Schaefer, H. W. T. van Vlijmen and M. Karplus.

 

569.  The Allosteric Mechanism of the Chaperonin GroEL: A Dynamic Analysis,

Proc. Natl. Acad. Sci. USA 95, 8502-8507 (1998),

by J. Ma and M. Karplus.

 

570.  Improving the Accuracy of Protein pKa Calculations: Conformational Averaging versus the Average

Structure,

Proteins: Structure, Function & Genetics 33, 145-158 (1998),

by H. W. T. van Vlijmen, M. Schaefer, and M. Karplus.

 

571.  Use of Quantitative Structure-Property Relationships to Predict the Folding Ability of Model Proteins,

Proteins: Structure, Function & Genetics 33, 177-203 (1998),

by A. R. Dinner, S.-S. So, and M. Karplus.

 

572.  Refolding of Potato Carboxypeptidase Inhibitor by Molecular Dynamics Simulations with Disulfide

Bond Constraints,

J. Mol. Biol. 284, 145-172 (1998),

by M. A. MartÌ-Renom, R. H. Stote, E. Querol, F. X. AvilÈs, and M. Karplus.

 

573.  Solution Conformations and Thermodynamics of Structured Peptides: Molecular Dynamics

Simulation with an Implicit Solvation Model,

J. Mol. Biol. 284, 835-847 (1998),

by M. Schaefer, C. Bartels, and M. Karplus.

 

574.  On the Potential Surface of the Locally Enhanced Sampling Approximation,

J. Chem. Phys. 109, 8809-8815 (1998),

by C. Stultz and M. Karplus.

 

575.  Yeast Chorismate Mutase in the R State: Simulations of the Active Site,

Proc. Natl. Acad. Sci. USA 95, 14640-14645 (1998),

by J. Ma, X. Zheng, G. Schnappauf, G. Braus, M. Karplus, and W. N. Lipscomb.

 

576.  Characterization of Flexible Molecules in Solution: the RGDW Peptide,

J. Mol. Biol. 284, 1641-1660 (1998),

by C. Bartels, R. H. Stote, and M. Karplus.

 

577.  CHARMM: The Energy Function and Its Parameterization with an Overview of the Program,

The Encyclopedia of Computational Chemistry, Vol. 1,

P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III,

P. R. Schreiner, editors, 271-277 (John Wiley & Sons: Chichester, 1998),

by A. D. MacKerell, Jr., B. Brooks, C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus.

 

578.  Protein Sidechain Conformer Prediction:  A Test of the Energy Function,

Folding & Design 3, 353-377 (1998),

by R. J. Petrella, T. Lazaridis, and M. Karplus.

 

579.  Protein Folding: Insights from Simulations,

Physica A 263, 389-391 (1999),

by M. Karplus.

 

580.  The Role of Bonded Terms in Free Energy Simulations: 1. Theoretical Analysis,

J. Phys. Chem. A 103, 103-118 (1999),

by S. Boresch and M. Karplus.

 

581.  The Role of Bonded Terms in Free Energy Simulations: 2. Calculation of their Influence on

Free Energy Differences of Solvation,

J. Phys. Chem. A 103, 119-136 (1999),

by S. Boresch and M. Karplus.

 

582.  Native Proteins are Surface-Molten Solids: Application of the Lindemann Criterion for the Solid

versus Liquid State,

J. Mol. Biol. 285, 1371-1377 (1999),

by Y. Zhou, D. Vitkup, and M. Karplus.

 

583.  T Cell Recognition of Hapten: Anatomy of T Cell Receptor Binding of a H-2Kd-Associated

Photoreactive Peptide Derivative,

J. Biol. Chem. 274, 3622-3631 (1999),

by B. Kessler, O. Michielin, C. L. Blanchard, I. Apostolou, C. Delarbre, G. Gachelin,

C. GrÈgoire, B. Malissen, J.-C. Cerottini, F. Wurm, M. Karplus, and I. F. Luescher.

 

584.  Adaptive Umbrella Sampling of the Potential Energy: Modified Updating Procedure of the

Umbrella Potential and Application to Peptide Folding,

Theor. Chem. Acc. 101, 62-66 (1999),

by C. Bartels, M. Schaefer, and M. Karplus.

 

585.  MCSS-Based Predictions of RNA Binding Sites,

Theor. Chem. Acc. 101, 131-137 (1999),

by F. Leclerc and M. Karplus.

 

586.  Solution Conformations of Structures Peptides: Continuum Electrostatics versus Distance-Dependent

Dielectric Functions,

Theor. Chem. Acc. 101, 194-204 (1999),

by M. Schaefer, C. Bartels, and M. Karplus.

 

587.  Factors that Affect the Folding Ability of Proteins,

Proteins: Structure, Function & Genetics 35, 34-40 (1999),

by A. R. Dinner, V. Abkevich, E. Shakhnovich and M. Karplus.

 

588.  A Comparative Study of Ligand-Receptor Complex Binding Affinity Prediction Methods Based on

Glycogen Phosphorylase Inhibitors,

J. Computer-Aided Molecular Design 13, 243-258 (1999),

by S.-S. So and M. Karplus.

 

589.  Effective Energy Function for Proteins in Solution,

Proteins: Structure, Function & Genetics 35, 133-152 (1999),

by T. Lazaridis and M. Karplus.

 

590.  Proteins Reactions and Conformational Change: Simple, Complex, or Both?

Simplicity and Complexity in Proteins and Nucleic Acids,

H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors, Chapter 8, 139-177

(Dahlem University Press, 1999),

by M. Karplus.

 

591.  The Fundamentals of Protein Folding: Bringing Together Theory and Experiment,

Current Opinion in Structural Biology 9, 92-101 (1999),

by C. M. Dobson and M. Karplus.

 

592.  Forced Unfolding of Fibronectin Type 3 Modules: An Analysis by Biased Molecular Dynamics

Simulations,

J. Mol. Biol. 288, 441-459 (1999),

by E. Paci and M. Karplus.

 

593.  Discrimination of the Native from Misfolded Protein Models with an Energy Function Including

Implicit Solvation,

J. Mol. Biol. 288, 477-487 (1999),

by T. Lazaridis and M. Karplus.

 

594.  Comment on: 'The Entropy Cost of Protein Association',

Protein Engineering 12, 185-186 (1999),

by M. Karplus and J. Janin.

 

595.  Analysis of Calculated Normal Modes of a Set of Native and Partially Unfolded Proteins,

J. Phys. Chem. B 103, 3009-3021 (1999),

by H.W.T. van Vlijmen and M. Karplus.

 

596.  New Methods for Accurate Prediction of Protein Secondary Structure,

Proteins: Structure, Function & Genetics 35, 293-306 (1999),

by J.-M. Chandonia and M. Karplus.

 

597.  A Hybrid QM-MM Potential Employing Hartree-Fock or Density Functional Methods in the

Quantum Region,

J. Phys. Chem. A 103, 3462-3471 (1999),

by P. D. Lyne, M. Hodoscek, and M. Karplus.

 

598.  The Calorimetric Criterion for a Two-State Process Revisited,

Protein Science 8, 1064-1074 (1999),

by Y. Zhou, C. K. Hall, and M. Karplus.

 

599.  Heat Capacity and Compactness of Denatured Proteins,

Biophys. Chem. 78, 207-217 (1999),

by T. Lazaridis and M. Karplus.

 

600.  Structural Details of Urea Binding to Barnase: A Molecular Dynamics Analysis,

Structure with Folding & Design 7, 477-488 (1999),

by A. Caflisch and M. Karplus.

 

601.  Mechanism of Alkaline Hydrolysis of Cyclic and Acyclic Sulfates: An Ab Initio Study with Solvation

Correction,

J. Am. Chem. Soc. 121, 5548-5558 (1999),

by X. Lopez, A. Dejaegere, and M. Karplus.

 

602.  Retinoic Acid Receptor: A Simulation Analysis of Retinoic Acid Binding and the Resulting

Conformational Changes,

J. Mol. Biol. 291, 101-115 (1999),

by A. Blondel, J.-P. Renaud, S. Fischer, D. Moras, and M. Karplus.

 

603.  Is Protein Unfolding the Reverse of Protein Folding? A Lattice Simulation Analysis,

J. Mol. Biol. 292, 403-419 (1999),

by A. R. Dinner and M. Karplus.

 

604.  Understanding b-Hairpin Formation,

Proc. Natl. Acad. Sci. USA 96, 9068-9073 (1999),

by A. R. Dinner, T. Lazaridis and M. Karplus.

 

605.  A Poisson-Boltzmann Study of Charge Insertion in an Enzyme Active Site: The Effect of Dielectric

Relaxation,

J. Phys. Chem. B 103, 6142-6156 (1999),

by T. Simonson, G. Archontis, and M. Karplus.

 

606.  The Thermodynamics and Kinetics of Protein Folding: A Lattice Model Analysis of Multiple

Pathways with Intermediates,

J. Phys. Chem. B 103, 7976-7994 (1999),

by A. R. Dinner and M. Karplus.

 

607.  Folding of a Model Three-Helix Bundle Protein: A Thermodynamic and Kinetic Analysis,

J. Mol. Biol. 293, 917-951 (1999),

by Y. Zhou and M. Karplus.

 

608.  Interpreting the Folding Kinetics of Helical Protein,

Nature 401, 400-403 (1999),

by Y. Zhou and M. Karplus.

 

609.  Internal and Overall Peptide Group Motion in Proteins: Molecular Dynamics Simulations for

Lysozyme Compared with Results from X-ray and NMR Spectroscopy,

J. Am. Chem. Soc. 121, 9645-9658 (1999),

by M. Buck and M. Karplus.

 

610.  Reply to the Paper by StachÛ et al. "On the Elber-Karplus Reaction Path-Following

Method and Related Procedures,"

Chem. Phys. Letters 311, 335-340 (1999),

by R. Elber and M. Karplus.

 

611.  Use of Quantitative Structure-Property Relationship to Design Larger Model Proteins that Fold Rapidly,

Protein Eng. 12, 909-917 (1999),

by A. R. Dinner, E. Verosub, and M. Karplus.

 

612.  A Smooth Solvation Potential Based on the Conductor-Like Screening Model,

J. Phys. Chem. A 103, 11060-11079 (1999),

by D. York and M. Karplus.

 

613.  Determination of Equilibrium Properties of Biomolecular Systems Using Multidimensional Adaptive

Umbrella Sampling,

J. Chem. Phys. 111, 8048-8067 (1999),

by C. Bartels, M. Schaefer and M. Karplus.

 

614.  MCSS Functionality Maps for a Flexible Protein,

Proteins: Structure, Function & Genetics 37, 512-529 (1999),

by C. M. Stultz & M. Karplus.

 

615.  Determination of the pKa of the 2'‑Hydroxyl Group of a Phophorylated Ribose: Implications for the

Mechanism of Hammerhead Ribozyme Catalysis,

J. Am. Chem. Soc. 122, 166-167 (2000),

by P. Lyne and M. Karplus.

 

616.  Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior,

J. Phys. Chem. B 104, 11-27 (2000),

by M. Karplus.

 

617.  Ab Initio QM/MM Study of the Citrate Synthase Mechanism. A Low-Barrier Hydrogen Bond Is Not

Involved,

J. Am. Chem. Soc. 122, 534-535 (2000),

by A. J. Mulholland, P. D. Lyne and M. Karplus.

 

618.  Solvent Mobility and the Protein 'Glass' Transition,

Nature Struc. Biol. 7, 34-38 (2000),

by D. Vitkup, D. Ringe, G. A. Petsko, and M. Karplus.

 

619.  Multiple Conformations of RGDW and dRGDW: A Theoretical Study and Comparison with

NMR Results,

J. Phys. Chem. B 104, 1624-1636 (2000),

by R. H. Stote, A. P. Dejaegere, J.-F. LefËvre, and M. Karplus.

 

620.  Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches,

J. Phys. Chem. A 104, 1720-1735 (2000),

by N. Reuter, A. Dejaegere, B. Maigret, and M. Karplus.

 

621.  Molecular Properties from Combined QM/MM Methods. I. Analytical Second Derivative and

Vibrational Calculations,

J. Chem. Phys. 112, 1133-1149 (2000),

by Q. Cui and M. Karplus.

 

622.  Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules,

J. Phys. Chem. B 104, 3721-3743 (2000),

by Q. Cui and M. Karplus.

 

623.  Design of Dimerization Inhibitors of HIV-1 Aspartic Proteinase: A Computer-Based Combinatorial

Approach,

J. Computer-Aided Molecular Design 14, 161-179 (2000),

by A. Caflisch, H. J. Schramm, and M. Karplus.

 

624.  Effective Energy Functions for Protein Structure Prediction,

Current Opinion in Structural Biology  10, 139-145 (2000),

by T. Lazaridis and M. Karplus.

 

625.  Quantitative Structure-Activity Relationship Studies of Progesterone Receptor Binding Steroids,

J. Chem. Inf. & Comp. Sci. 40, 762-772 (2000),

by S.-S. So, S. P. van Helden, V. J. van Geerestein, and M. Karplus.

 

626.  Dynamics Ligand Design and Combinatorial Optimization: Designing Inhibitors to Endothiapepsin,

Proteins: Structure, Function & Genetics 40, 258-289 (2000),

by C. M. Stultz and M. Karplus.

 

627.  Understanding Protein Folding via Free-Energy Surfaces from Theory and Experiment,

TiBS 25, 331-339 (2000),

by A. R. Dinner, A. Sali, L. J. Smith, C. M. Dobson, and M. Karplus.

 

628.  Modeling of the TCR-MHC-Peptide Complex,

J. Mol. Biol. 300, 1205-1237 (2000),

by O. Michielin, I. Luescher, and M. Karplus.

 

629.  Unfolding Proteins by External Forces and Temperature: The Importance of Topology and Energetics,

Proc. Natl. Acad. Sci. USA 97, 6521-6526 (2000),

by E. Paci and M. Karplus.

 

630.  A Dynamic Model for the Allosteric Mechanism of GroEL,

J. Mol. Biol. 302, 303-313 (2000),

by J. Ma, P. B. Sigler, Z. Xu, and M. Karplus.

 

631.  Structures of Scrambled Disulfide Forms of the Potato Carboxypeptidase Inhibitor Predicted by

Molecular Dynamics Simulations with Constraints,

Proteins: Structure, Function & Genetics 40, 482-493 (2000),

by M. A. MartÌ-Renom, R. H. Stote, E. Querol, F. X. AvilÈs, and M. Karplus.

 

632.  Protein Motions at Zero-Total Angular Momentum: The Importance of Long-Range Correlations,

Biophys. J. 79, 2902-2908 (2000),

by Y. Zhou, M. Cook, and M. Karplus.

 

633.  A Limiting-Case Study of Protein Structure Prediction: Energy-Based Searches of Reduced

Conformational Space,

J. Phys. Chem. B 104, 11370-11378 (2000),

by R. J. Petrella and M. Karplus.

 

634.  Microscopic Basis of Macromolecular Thermodynamics,

Thermodynamics in Biology, E. Di Cera, editor, 3-48 (Oxford University Press, 2000),

by T. Lazaridis and M. Karplus.

 

635.  The Roles of Stability and Contact Order in Determining Protein Folding Rates,

Nature Struct. Biol. 8, 21-22 (2001),

by A. R. Dinner and M. Karplus.

 

636.  Exploration of Partially Unfolded States of Human a-Lactalbumin by Molecular Dynamics

Simulation, J. Mol. Biol. 306, 329-347 (2001),

by E. Paci, L. J. Smith, C. M. Dobson and M. Karplus.

 

637.  A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding

(SCC-DFTB) Method,

J. Phys. Chem. B 105, 569-585 (2001),

by Q. Cui, M. Elstner, E. Kaxiras, T. Frauenheim, and M. Karplus.

 

638.  Three Key Residues Form a Critical Contact Network in a Protein Folding Transition State,

Nature 409, 641-645 (2001),

by M. Vendruscolo, E. Paci. C. M. Dobson, and M. Karplus.

 

639.  Binding Free Energies and Free Energy Components from Molecular Dynamics and

Poisson-Boltzmann Calculations. Application to Amino Acid Recognition by Aspartyl-tRNA

Synthetase,

J. Mol. Biol. 306, 307-327 (2001),

by G. Archontis, T. Simonson, and M. Karplus.

 

640.  Triosephosphate Isomerase: A Theoretical Comparison of Alternative Pathways,

J. Am. Chem. Soc. 123, 2284-2290 (2001),

by Q. Cui and M. Karplus.

 

641.  Foreward,

Computational Biochemistry and Biophysics, O. M. Becker, A. D. MacKerell, Jr., B. Roux, and

M. Watanabe, editors, iii-v (Marcel Dekker, Inc., 2001),

by M. Karplus.

 

642.  Normal Mode Analysis of Large Systems with Icosahedral Symmetry: Application to (Dialanine)60

in Full and Reduced Basis Set Implementations,

J. Chem. Phys. 115, 691-698 (2001),

by H. W. T. Van Vlijmen and M. Karplus.

 

643.  Substrate Conformational Transitions in the Active Site of Chorismate Mutase: Their Role in the

Catalytic Mechanism,

Proc. Natl. Acad. Sci. USA 98, 9032-9037 (2001),

by H. Guo, Q, Cui, W. N. Lipscomb, and M. Karplus.

 

644.  Evaluation of Designed Ligands by a Multiple Screening Method: Application to Glycogen

Phosphorylase Inhibitors Constructed with a Variety of Approaches,

J. Computer-Aided Molecular Design 15, 613-647 (2001),

by S.-S. So and M. Karplus.

 

645.  Simulation of Quantum Systems Using Path Integrals in a Generalized Ensemble,

Chem. Phys. Letters 346, 274-282 (2001),

by I. Andricioaei, J. E. Straub, and M. Karplus.

 

646.  The Energetics of Off-Rotamer Protein Sidechain Conformation,

J. Mol. Biol. 312, 1161-1175 (2001),

by R. J. Petrella and M. Karplus.

 

647.  Uracil-DNA Glycosylase Acts by Substrate Autocatalysis,

Nature 413, 752-755 (2001),

by A. R. Dinner, G. M. Blackburn, and M. Karplus.

 

648.  On the Calculation of Entropy from Covariance Matrices of the Atomic Fluctuations,

J. Chem. Phys. 115, 6289-6292 (2001),

by I. Andricioaei and M. Karplus.

 

649.  Effective Atom Volumes for Implicit Solvent Models: Comparison between Voronoi Volumes and

Minimum Fluctuation Volumes,

J. Comp. Chem. 22, 1857-1879 (2001),

by M. Schaefer, C. Bartels, F. Leclerc, and M. Karplus.

 

650.  Crystal Structures of Two Closely Related but Antigenically Distinct HLA-A2/Melanocyte-Melanoma

Tumor-Antigen Peptide Complexes,

J. Immunol. 167, 3276-3284 (2001),

by P. Sliz, O. Michielin, J.-C. Cerottini, I. Luescher, P. Romero, M. Karplus, and D. C. Wiley.

 

651.  Forces and Energetics of Hapten-Antibody Dissociation: A Biased Molecular Dynamics

Simulation Study,

J. Mol. Biol. 314, 589-605 (2001),

by E. Paci, A. Caflisch, A. Pl¸ckthun, and M. Karplus.

 

652.  Hydrogen Bond Energetics: A Simulation and Statistical Analysis of N-Methyl Acetamide (NMA),

Water, and Human Lysozyme,

J. Phys. Chem. B 105, 11000-11015 (2001),

by M. Buck and M. Karplus.

 

653.  Solvent Effects on the Reaction Coordinate of the Hydrolysis of Phosphates and Sulfates:

Application of Hammond and Anti-Hammond Postulates to Understand Hydrolysis in Solution,

J. Am. Chem. Soc. 123, 11755-11763 (2001),

by X. Lopez, A. Dejaegere, and M. Karplus.

 

654.  Synthesis of a Novel Diarylphosphinic Acid: A Distorted Ground State Mimic and Transition State

Analogue for Amide Hydrolysis,

Tetrahedron 57, 10299-10307 (2001),

by M. Schuman, X. Lopez, M. Karplus, and V. Gouverneur.

 

655.  Comment on the Communication "The Key to Solving the Protein-Folding Problem Lies in an

Accurate Description of the Denatured State" by van Gunsteren et al.,

Angew. Chem. Int. Ed. 40, 4615-4616 (2001),

by A. R. Dinner and M. Karplus.

 

656.  Functional Group Placement in Protein Binding Sites: A Comparison of GRID and MCSS,

J. Computer-Aided Molecular Design 15, 935-960 (2001),

by R. Bitetti-Putzer, D. Joseph-McCarthy, J. M. Hogle, and M. Karplus.

 

657.  Use of MCSS to Design Small Targeted Libraries: Application to Picornavirus Ligands,

J. Am. Chem. Soc. 123, 12758-12769 (2001),

by D. Joseph-McCarthy, S. K. Tsang, D. J. Filman, J. M. Hogle, and M. Karplus.

 

658.  Statistical Analysis of Protein Folding Kinetics,

Computational Methods for Protein Folding: A Special Volume of

Adv. Chem. Physics 120, 1-34 (2002),

by A. R. Dinner, S.-S. So, and M. Karplus.

 

659.  Quantum Mechanical/Molecular Mechanical Studies of the Triosephosphate Isomerase-Catalyzed

Reactions: Verification of Methodology and Analysis of the Reaction Mechanisms,

J. Phys. Chem. B 106, 1768-1798 (2002),

by Q. Cui and M. Karplus.

 

660.  The Distance Fluctuation Criterion for Melting: Comparison of Square-Well and Morse Potential

Models for Clusters and Homopolymers,

J. Chem. Phys. 116, 2323-2329 (2002),

by Y. Zhou, M. Karplus, K. D. Ball, and R. S. Berry.

 

661.  Simulation of Proton Transfer along Ammonia Wires: An "ab initio" and Semiempirical Density

Functional Comparison of Potentials and Classical Molecular Dynamics,

J. Chem. Phys. 116, 2572-2585 (2002),

by M. Meuwly and M. Karplus.

 

662.  Why Protein R-factors Are So Large: A Self-Consistent Analysis,

Proteins: Structure, Function & Genetics 46, 345-354 (2002),

by D. Vitkup, D. Ringe, M. Karplus, and G. A. Petsko.

 

663.  A Theoretical Analysis of the Proton and Hydride Transfer in Liver Alcohol Dehydrogenase (LADH),

J. Phys. Chem. B 106, 2721-2740 (2002),

by Q. Cui, M. Elstner, and M. Karplus.

 

664.  Potential Energy Surfaces and Conformational Transitions in Biomolecules: A Successive

Confinement Approach Applied to a Solvated Tetrapeptide,

Phys. Rev . Letters 88, 038101.1-4 (2002),

by S. V. Krivov, S. F. Chekmarev, and M. Karplus.

 

665.  Quantum Mechanics/Molecular Mechanics Studies of the Triosephosphate Isomerase-Catalyzed

Reactions: Effect of Geometry and Tunneling on Proton-Transfer Rate Constants,

J. Am. Chem. Soc. 124, 3093-3124 (2002),

by Q. Cui and M. Karplus.

 

666.  Relation between Sequence and Structure of HIV-1 Protease Inhibitor Complexes: A Model System

for the Analysis of Protein Flexibility,

J. Mol. Biol. 315, 21-52 (2002),

by V. Zoete, O. Michielin, and M. Karplus.

 

667.  Theoretical Evaluation of pKa in Phosphoranes: Implications for Phosphate Ester Hydrolysis,

J. Am. Chem. Soc. 124, 5010-5018 (2002),

by X. Lopez, M. Schaefer, A. Dejaegere, and M. Karplus.

 

668.  Application of the Diffusion-Collision Model to the Folding of Three-Helix Bundle Proteins,

J. Mol. Biol. 318, 199-215 (2002),

by S. A. Islam, M. Karplus, and D. L. Weaver.

 

669.  Native and Non-Native Interactions Along Protein Folding and Unfolding Pathways,

Proteins: Structure, Function & Genetics 47, 379-392 (2002),

by E. Paci, M. Vendruscolo, and M. Karplus.

 

670.  Small-World View of the Amino Acids that Play a Key Role in Protein Folding,

Phys. Rev. E 65, 061910.1-061910.4 (2002),

by M. Vendruscolo, N. V. Dokholyan, E. Paci, and M. Karplus.

 

671.  A Dynamic Analysis of the Rotation Mechanism for Conformational Change in F1-ATPase,

Structure 10, 921-931 (2002),

by J. Ma, T. C. Flynn, Q. Cui, A.G.W. Leslie, J. E. Walker, and M. Karplus.

 

672.  Molecular Dynamics Simulations of Biomolecules,

Accts. Chem. Res. 35, 321-323 (2002),

by M. Karplus.

 

673.  Free Energy Simulations Come of Age: Protein-Ligand Recognition,

Accts. Chem. Res. 35, 430-437 (2002),

by T. Simonson, G. Archontis, and M. Karplus.

 

674.  NO Rebinding to Myoglobin: A Reactive Molecular Dynamics Study,

Biophys. Chem. 98, 183-207 (2002),

by M. Meuwly, O. M. Becker, R. Stote, and M. Karplus.

 

675.  Promoting Modes and Demoting Modes in Enzyme-Catalyzed Proton Transfer Reactions:  A Study of

Models and Realistic Systems,

J. Phys. Chem. B 106, 7927-7947 (2002),

by Q. Cui and M. Karplus.

 

676.  Structure Activity Relationship by NMR and by Computer: A Comparative Study,

J. Am. Chem. Soc. 124, 11073-11084 (2002),

by F. Sirockin, C. Sich, S. Improta, M. Schaefer, V. Saudek, N. Froloff, M. Karplus, and A. Dejaegere.

 

677.  Conformational Analysis of a Stereochemically Complete Set of Cis-enediol Peptide Analogues,

J. Am. Chem. Soc. 124, 11131-11141 (2002),

by O. Michielin, V. Zoete, T. M. Gierasch, J. Eckstein, A. Napper, G. Verdine, and M. Karplus.

 

678.  Theoretical Studies on the Hydrolysis of Phosphate Diesters in the Gas Phase, Solution, and RNase A,

Internat. J. Quantum Chem. 86, 10-26 (2002),

by X. Lopez, D. M. York, A. Dejaegere, and M. Karplus.

 

679.  Combining ab initio and Density Functional Theories with Semiempirical Methods,

J. Chem. Phys. 117, 5617-5631 (2002),

by Q. Cui, H. Guo, and M. Karplus.

 

680.  Molecular Dynamics Simulations of Biomolecules,

Nature Struc. Biol. 9, 646-652 (2002),

by M. Karplus and J. A. McCammon.

 

681.  Mechanical Unfolding of a Titin Ig Domain: Structure of Unfolding Intermediate Revealed by

Combining AFM, Molecular Dynamics Simulations, NMR and Protein Engineering,

J. Mol. Biol. 322, 841-849 (2002),

by S. B. Fowler, R. B. Best, J. L. Toca Herrera, T. J. Rutherford, A. Steward, E. Paci, M. Karplus,

and J. Clarke.

 

682.  Translocation Mechanism of Long Sugar Chains Across the Maltoporin Membrane Channel,

Structure 10, 1273-1284 (2002),

by R. Dutzler, T. Schirmer, M. Karplus, and S. Fischer.

 

683.  Free Energy Disconnectivity Graphs: Application to Peptide Models,

J. Chem. Phys. 117, 10894-10903 (2002),

S. V. Krivov and M. Karplus.

 

684.  Validity of Go Models: Comparison with a Solvent-Shielded Empirical Energy Decomposition,

Biophys. J. 83, 3032-3038 (2002),

by E. Paci, M. Vendruscolo, and M. Karplus.

 

685.  Determination of a Transition State at Atomic Resolution from Protein Engineering Data,

J. Mol. Biol. 324, 151-163 (2002),

by E. Paci, M. Vendruscolo, C. M. Dobson, and M. Karplus.

 

686.  Binding Free Energy Differences in a TCR-Peptide-MHC Complex Induced by a Peptide Mutation:

A Simulation Analysis,

J. Mol. Biol. 324, 547-569 (2002),

by O. Michielin and M. Karplus.

 

687.  An Improved Method for Non-Bonded List Generation: Rapid Determination of Near-Neighbor Pairs,

J. Comp. Chem. 24, 222-231 (2003),

by R. J. Petrella, I. Andricioaei, B. R. Brooks, and M. Karplus.

 

688.  Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and

Elucidation of the Role of Interfacial Water,

J. Mol. Biol. 326, 593-606 (2003),

by Y. Zhou, H. Zhou, and M. Karplus.

 

689.  Self-Consistent Determination of the Transition State for Protein Folding. Application to a Fibronectin

Type III domain,

Proc. Natl. Acad. Sci. USA 100, 394-399 (2003),

by E. Paci, J. Clarke, A. Stewart, M. Vendruscolo, and M. Karplus.

 

690.  The Missing Link between Thermodynamics and Structure in F1‑ATPase,

Proc. Natl. Acad. Sci. USA 100, 874-879 (2003),

by W. Yang, Y. Q. Gao, Q. Cui, J. Ma, and M. Karplus.

 

691.  Molecular Dynamics of Biological Macromolecules: A Brief History and Perspective,

Biopolymers 68, 350-358 (2003),

by M. Karplus.

 

692.  Product-Assisted Catalysis in Base-Excision DNA Repair,

Nature Struc. Biol. 10, 204-211 (2003),

by J. C. Fromme, S. D. Bruner, W. Yang, M. Karplus, and G. L. Verdine.

 

693.  Understanding the Role of Active Site Residues in Chorismate Mutase Catalysis from Molecular

Dynamics Simulations,

Angew. Chem. Int. Ed. 42, 1508-1511 (2003),

by H. Guo, Q. Cui, W. N. Lipscomb, and M. Karplus.

 

694.  Self-Guided Enhanced Sampling Methods for Thermodynamic Averages,

J. Chem. Phys. A 118, 1074-1084 (2003),

by I. Andricioaei, A. R. Dinner, and M. Karplus.

 

695.  Alkaline Hydrolysis of Amide Bonds: Effect of Bond Twist and Nitrogen Pyramidalization,

J. Phys. Chem. A 107, 2304-2315 (2003),

by X. Lopez, J. I. Mujika, G.M. Blackburn, and M. Karplus.

 

696.  Is "Proton Wire" Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase,

J. Phys. Chem. B 107, 1071-1078 (2003),

by Q. Cui and M. Karplus.

 

697.  A Charge-Scaling Procedure to Treat Solvent in QM/MM Simulations,

Theor. Chem. Acc. 109, 118-124 (2003),

by A. R. Dinner, X. Lopez, and M. Karplus.

 

698.  Modeling Zinc in Biomolecules with the Self Consistent Charge-Density Functional Tight Binding

(SCC-DFTB) Method: Applications to Structural and Energetical Analysis,

J. Comp. Chem. 24, 565-581 (2003),

by M. Elstner, Q. Cui, P. Munih, E. Kaxiras, T. Frauenheim, and M. Karplus.

 

699.  Thermodynamics of Protein Folding: A Microscopic View,

Biophys. Chem. 100, 367-395 (2003),

by T. Lazaridis and M. Karplus.

 

700.  Generalized Ensembles Serve to Improve the Convergence of Free Energy Simulations,

Chem. Phys. Ltrs. 377, 633-641 (2003),

by R. Bitetti-Putzer, W. Yang, and M. Karplus.

 

701.  DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids,

Biophys. J. 84, 1421-1449 (2003),

by S. Y. Reddy, F. Leclerc, and M. Karplus.

 

702.  Absolute Binding Free Energies: A Quantitative Approach for Their Calculation,

J. Phys. Chem. B 107, 9535-9551 (2003),

by S. Boresch, F. Tettinger, M. Leitgeb, and M. Karplus.

 

703.  Theoretical Investigations of Ferredoxin I: The Possible Role of Internal Water Molecules in the

Coupled Electron Proton Transfer Reaction,

Faraday Discussions 124, 297-313 (2003),

by M. Meuwly and M. Karplus.

 

704.  A Model for the Cooperative Free Energy Transduction and Kinetics of ATP Hydrolysis by

F1‑ATPase,

Proc. Natl. Acad. Sci. USA 100, 11339-11344 (2003),

by Y. Q. Gao, W. Yang, R. A. Marcus, and M. Karplus.

 

705.  Catalysis and Specificity in Enzymes: A Study of Triosephosphate Isomerase and Comparison with

Methyl Glyoxal Synthase,

Adv. Protein Chem. 66, 315-372 (2003),

by Q. Cui and M. Karplus.

 

706.  Rare Fluctuations of Native Proteins Sampled by Equlibrium Hydrogen Exchange,

J. Am. Chem. Soc. 125, 15686-15687 (2003),

by M. Vendruscolo, E. Paci, C. M. Dobson, and M. Karplus.

 

707.  Protein-Ligand Binding Free Energy Estimation Using Molecular Mechanics and Continuum

Electrostatics. Application to HIV-1 Protease Inhibitors,

J. Computer-Aided Molecular Design 17, 861-880 (2003),

by V. Zoete, O. Michielin, and M. Karplus.

 

708.  Structures and Relative Free Energies of Partially Folded States of Proteins,

Proc. Natl. Acad. Sci. USA 100, 14817-14821 (2003),

by M. Vendruscolo, E. Paci, M. Karplus, and C. M. Dobson.

 

709.  How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations,

Science 303, 186-195 (2004),

by M. Garcia-Viloca, J. Gao, M. Karplus, and D. G. Truhlar.

 

710.  Free Energy Simulations: Use of Reverse Cumulative Averaging to Determine the Equilibrated Region

and the Time Required for Convergence,

J. Chem. Phys. 120, 2618-2628 (2004),

by W. Yang, R. Bitetti-Putzer, and M. Karplus.

 

711.  Comparison of the Transition States Ensembles for Folding of Im7 and Im9 Determined Using

All-Atom Molecular Dynamics Simulations with ¯ Value Restraints,

Proteins: Structure, Function & Bioinformatics 54, 513-525 (2004),

by E. Paci, C. T. Friel, K. Lindorff-Larsen, S. E. Radford, M. Karplus, and M. Vendruscolo.

 

712.  The Role of Carbon-Donor Hydrogen Bonds in Stabilizing Tryptophan Conformations,

Proteins: Structure, Function & Bioinformatics 54, 716-726 (2004),

by R. J. Petrella and M. Karplus.

 

713.  Investigation of Glucose Binding Sites on Insulin,

Proteins: Structure, Function, & Bioinformatics 55, 568-581 (2004),

by V. Zoete, M. Meuwly, and M. Karplus.

 

714.  X-ray Structural and Simulation Analysis of a Protein Mutant: The Value of a Combined Approach,

Proteins: Structure, Function & Bioinformatics 55, 733-742 (2004),

by C. Mattos, J. D. Cohen, D. F. Green, B. Tidor, and M. Karplus.

 

715.  Biomolecular Motors: the F₁-ATPase Paradigm,

Current Opinion in Structural Biology 14, 250-259 (2004),

by M. Karplus and Y. Q. Gao.

 

716.  Theoretical Investigations on Azotobacter vinelandii Ferredoxin I: Effects of Electron Transfer on

Protein Dynamics,

Biophys. J. 86, 1987-2007 (2004),

by M. Meuwly and M. Karplus.

 

717.  Chaperoned Alchemical Free Energy Simulations: A General Method for QM, MM, and QM/MM

Potentials,

J. Chem. Phys. 120, 9450-9453 (2004),

by W. Yang, R. Bitetti-Putzer, and M. Karplus.

 

718.  Increasing Normal Modes Analysis Accuracy: The SPASIBA Spectroscopic Force Field

Introduced into the CHARMM Program,

J. Phys. Chem. A 108, 4019-4029 (2004),

by P. Lagant, D. Nolde, R. Stote, G. Vergoten, and M. Karplus.

 

719.  The Origin of Protein Sidechain Order Parameter Distributions,

J. Am. Chem. Soc. 126, 7734-7735 (2004),

by R. B. Best, J. Clarke, and M. Karplus.

 

720.  The Unfolding Action of GroEL on a Protein Substrate,

Biophys. J. 87, 562-573 (2004),

by A. van der Vaart, J. Ma, and M. Karplus.

 

721.  The Crystallographic Structure of the Aldose Reductase-IDD552 Complex Shows Direct Proton

Donation from Tyrosine 48,

Acta Crystallogr D Biol Crystallogr 60, 1347-1354 (2004),

by F. Ruiz, I. Hazemann, A. Mitschler, A. Joachimiak, T. Schneider, M. Karplus, and A. Podjarny.

 

722.  A Normal Mode Analysis of Structural Plasticity in the Biomolecular Motor F1‑ATPase,

J. Mol. Biol. 340, 345-372 (2004),

by Q. Cui, G. Li, J. Ma, and M. Karplus.

 

723.  A Comparison of the Dynamic Behavior of Monomeric and Dimeric Insulin Shows Structural

Rearrangements in the Active Monomer,

J. Mol. Biol. 342, 913-929 (2004),

by V. Zoete, M. Meuwly, and M. Karplus.

 

724.  Kinetic Control of Dimer Structure Formation in Amyloid Fibrillogenesis,

Proc. Natl. Acad. Sci. USA 101, 12916-12921 (2004),

by W. Hwang, S. Zhang, R. D. Kamm, and M. Karplus.

 

725.  Dependence of DNA Polymerase Replication Rate on External Forces: A Model Based on Molecular

Dynamics Simulations,

Biophys. J. 87, 1478-1497 (2004),

by I. Andricioaei, A. Goel, D. Herschbach, and M. Karplus.

 

726.  Hidden Complexity of Free Energy Surfaces for Peptide (Protein) Folding,

Proc. Natl. Acad. Sci. USA 101, 14766-14770 (2004),

by S. V. Krivov and M. Karplus.

 

727.  The Role of Sequence and Structure in Protein Folding Kinetics: the Diffusion-Collision Model

Applied to Proteins L and G,

Structure 12, 1833-1845 (2004),

by S. A. Islam, M. Karplus, and D. L. Weaver.

 

728.  Calculation of the Aqueous Solvation Energy and Entropy, as well as Free Energy, of Simple

Polar Solutes,

J. Chem. Phys. 121, 9539-9548 (2004),

by S. Wan, R. H. Stote, and M. Karplus.

 

729.  Protein Structural Transitions and their Functional Role,

Phil. Trans. R. Soc. A 363, 331-356 (2005),

by M. Karplus, Y. Q. Gao, J. Ma, A. van der Vaart, and W. Yang.

 

730.  Electrostatic Energies and Forces Computed Without Explicit Interparticle Interactions: A Linear

Time Complexity Formulation,

J. Comput. Chem. 26, 755-787 (2005),

by R. J. Petrella and M. Karplus.

 

731.  Structure of a Repair Enzyme Interrogating Undamaged DNA Elucidates Recognition of

Damaged DNA,

Nature 434, 612-618 (2005),

by A. Banerjee, W. Yang, M. Karplus and G. L. Verdine.

 

732.  Folding Time Distributions as an Approach to Protein Folding Kinetics,

J. Phys. Chem. B 109, 5312-5330 (2005),

by S. F. Chekmarev, S. V. Krivov and M. Karplus.

 

733.  Simulation of Conformational Transitions by the Restricted Perturbation-Targeted

Molecular Dynamics Method,

J. Chem. Phys. 122, 114903.1-114903.6 (2005),

by A. van der Vaart and M. Karplus.

 

734.  What Contributions to Protein Side-chain Dynamics are Probed by NMR Experiments? A Molecular

Dynamics Simulation Analysis,

J. Mol. Biol. 349, 185-203 (2005),

by R. B. Best, J. Clarke, and M. Karplus.

 

735.  Design, Synthesis, and Biological Evaluation of HSP90 Inhibitors Based on Conformational

Analysis of Radicicol and Its Analogues,

J. Am. Chem. Soc. 127, 6999-7004 (2005),

by E. Moulin, V. Zoete, S. Barluenga, M. Karplus, and N. Winssinger.

 

736.  Molecular Dynamics and Protein Function,

Proc. Natl. Acad. Sci. USA 102, 6679-6685 (2005),

by M. Karplus and J. Kuriyan.

 

737.  Normal Mode Calculations of Icosahedral Viruses with Full Dihedral Flexibility by Use of

Molecular Symmetry,

J. Mol. Biol. 350, 528-542 (2005),

by H. W. T. van Vlijmen and M. Karplus.

 

738.  Role of Conformational Heterogeneity in Domain Swapping and Adapter Function of the

Cks Proteins,

J. Biol. Chem. 280, 30448-30459 (2005).

by M. A. Seeliger, M. Spichty, S. E. Kelly, M. Bycroft, S.M.F. Freund, M. Karplus, and

L. S. Itzhaki.

 

739.  Transition State Contact Orders Correlate with Protein Folding Rates,

J. Mol. Biol. 352, 495-500 (2005),

by E. Paci, K. Lindorff-Larsen, C. M. Dobson, M. Karplus, and M. Vendruscolo.

 

740. Study of the Insulin Dimerization: Binding Free Energy Calculations and Per-Residue Free

Energy Decomposition,

Proteins: Structure, Function & Bioinformatics 61, 79-93 (2005),

by V. Zoete, M. Meuwly, and M. Karplus.

 

741.  Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model:

Adenylate Kinase,

J. Mol. Biol. 352, 807-822 (2005),

by P. Maragakis and M. Karplus.

 

742.  A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1‑ATPase,

Cell 123, 195-205 (2005),

by Y. Q. Gao, W. Yang, and M. Karplus.

 

743.  Glycogen Phosphorylase Inhibitors: A Free Energy Perturbation Analysis of Glucopyranose

Spirohydantoin Analogues,

Proteins: Structure, Function & Bioinformatics 61, 984-998 (2005),

by G. Archontis, K. A. Watson, Q. Xie, G. Andreou, E. D. Chrysina, S. E. Zographos, N. G. Oikonomakos, L. N. Johnson, and M. Karplus.

 

744.  Potential Energy Surface and Molecular Dynamics of MbNO: Existence of an Unsuspected FeON

Minimum,

J. Phys. Chem. B 109, 21118-21125 (2005),

by D. R. Nutt, M. Karplus, and M. Meuwly.

 

745.  The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis,

J. Mol. Biol. 356, 237-247 (2006),

by Y. Kong, J. Ma, M. Karplus, and W. N. Lipscomb.

 

746.  Two-Metal-Ion Mechanism for Hammerhead-Ribozyme Catalysis,

J. Phys. Chem. 110, 3395-3409 (2006),

by F. Leclerc and M. Karplus.

 

747.  Optimal Estimates of Free Energies from Multistate Nonequilibrium Work Data,

Phys. Rev. Letters 96, 100602.1-100602.4 (2006),

by P. Maragakis, M. Spichty, and M. Karplus.

 

748.  Foreward,

Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems,

Q. Cui and I. Bahar, editors, v-vii (Chapman & Hall/CRC Press, Boca Raton, Florida, 2006),

by M. Karplus.

 

749.  Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and

Elucidation of the Role of Interfacial Water,

in Allosteric Proteins: 40 Years with Monod-Wyman-Changeux 17, 191-211,

M. Brunori, G. Careri, J.-P. Changeux, and H. K. Schachman, editors

(Academia Nationale dei Lincei, Roma, 2006),

by Y. Zhou, H. Zhou and M. Karplus.

 

750.  Spinach on the Ceiling: A Theoretical Chemist's Return to Biology,

Ann. Rev. Biophys. & Biomolecular Struc. 35, 1-4 (2006),

by M. Karplus.

 

751.  Folding of Ubiquitin: A Simple Model Describes the Strange Kinetics,

J. Phys. Chem. B 110, 8865-8869 (2006),

by S. F. Chekmarev, S. V. Krivov, and M. Karplus.

 

752.  Distance Disorder in Proteins Is Caused by Trapping,

J. Phys. Chem. B 110, 9363-9367 (2006),

by G. Luo, I. Andricioaei, X. S. Xie, and M. Karplus.

 

753.  A Src-Like Inactive Conformation in the Abl Tyrosine Kinase Domain,

PLOS Biology 4, 0753-0767 (2006),

by N. M. Levinson, O. Kuchment, K. Shen, M. A. Young, M. Koldobskiy, M. Karplus, P. A. Cole, and J. Kuriyan.

 

754.  Conformational Sampling Via a Self-Regulating Effective Energy Surface,

J. Chem. Phys. 124, 174901-174915 (2006),

by R. Bitetti-Putzer, A. R. Dinner, W. Yang, and M. Karplus.

 

755.  Nucleophilic Attack on Phosphate Diesters: A Density Functional Study of In-Line Reactivity in

Dianionic, Monoanionic, and Neutral Systems,

J. Phys. Chem. B 110, 11525-11539 (2006),

by X. Lopez, A. Dejaegere, F. Leclerc, D. M. York, and M. Karplus.

 

756.  One Dimensional Free Energy Profiles of Complex Systems: Progress Variables that Preserve the

Barriers,

J. Phys. Chem. B 110, 12689-12698 (2006),

by S. V. Krivov and M. Karplus.

 

757.  Fragment Docking to Proteins with the Multi-Copy Simultaneous Search (MCSS) Methodology,

in Fragment-based Approaches in Drug Discovery, Chapter 7, 125-148,

W. Jahnke, D. A. Erlanson, R. Mannhold, H. Kubinyi, and G. Folkers, editors (2006),

by C. M. Stultz and M. Karplus.

 

758.  Implications of the Quaternay Twist Allosteric Model for the Physiology and Pathology of Nicotinic

Acetylcholine Receptors,

Proc. Natl. Acad. Sci. USA 103, 16965-16970 (2006),

by A. Taly, P.-J. Corringer, T. Grutter, L. Prado de Carvalho, M. Karplus, and J.-P. Changeux.

 

759.  Implications of Alternative Substrate Binding Modes for Catalysis by Uracil-DNA Glycosylase: An Apparent Discrepancy Resolved,

Biochemistry 45, 13687-13696 (2006),

by A. Ma, J. Hu, M. Karplus, and A. R. Dinner.

 

760.  Probing Polar Solvation Dynamics in Proteins: A Molecular Dynamics Simulation Analysis,

J. Phys. Chem. B 111, 1482-1490 (2007),

by A. A. Golosov and M. Karplus.

 

761.  Lattice Protein with an Amyloidogenic Latent State: Stability and Folding Kinetics,

J. Phys. Chem. B 111, 2675-2687 (2007),

by A. Y. Palyanov, S. V. Krivov, M. Karplus, and S. F. Chekmarev.

 

762.  Minimum Free Energy Pathways and Free Energy Profiles for Conformational Transitions Based on Atomistic Molecular Dynamics Simulations,

J. Chem. Phys. 126, 164106.1-164106.17 (2007),

by A. van der Vaart and M. Karplus.

 

763.  A Kinetic Model of Coordinated Myosin V,

Biochemistry 46, 6318-6330 (2007),

by Y. Wu, Y. Q. Gao, and M. Karplus.

 

764.  The Signaling Pathway of Rhodopsin,

Structure 15, 611-623 (2007),

by Y. Kong and M. Karplus.

 

765.  Ligand Design by a Combinatorial Approach Based on Modeling and Experiment:

Application to HLA-DR4,

J. Comput. Aided Mol. Des. 21, 395-418 (2007),

by E. Evensen, D. Joseph-McCarthy, G. A. Weiss, S. L. Schreiber, and M. Karplus.

 

766.  Importance of Metastable States in the Free Energy Landscapes of Polypeptide Chains,

Phys. Rev. Lett. 99, 178104 (2007),

by S. Auer, M. A. Miller, S. V. Krivov, C. M. Dobson, M. Karplus, and M. Vendruscolo.

 

767.  Intrinsic Motions Along an Enzymatic Reaction Trajectory,

Nature 450, 838-844 (2007),

by V.Thai, K. Henzler-Wildman, M. Lei, M. Wunderlich, M. Wolf-Watz, T. Fenn, E. Pozharski, M. A. Wilson, G. A. Petsko, M. Karplus, C. G. H¸bner, and D. Kern.

 

768.  A Hierarchy of Timescales in Protein Dynamics Linked to Enzyme Catalysis,

Nature 450, 913-916 (2007),

by K. Henzler-Wildman, M. Lei, V. Thai, M. Karplus, and D. Kern.

 

769.  Force Generation in Kinesin Hinges on Cover-Neck Bundle Formation,

Structure 16, 62-71 (2008),

by W. Hwang, M. J. Lange, and M. Karplus.

 

770.  Hydrodynamics of Protein Folding,

Phys. Rev. Lett. 100, 18107-1-18107-4 (2008),

by S. F. Chekmarev, A. Y. Palyanov, and M. Karplus.

 

771.  How Subunit Coupling Produces the g-Subunit Rotary Motion in F₁-ATPase,

Proc. Natl. Acad. Sci. USA 105, 1192-1197 (2008),

by J. Pu and M. Karplus.

 

772.  The Elastic Properties of the Structurally Characterized Myosin II S2 Sub-domain: A Molecular

Dynamics and Normal Mode Analysis,

Biophysical Journal 94, 3779-3789 (2008),

by I. Adamovic, S. M. Mijailovich, and M. Karplus.

 

773.  Bayesian Estimates of Free Energies from Nonequilibrium Work Data in the Presence of

Instrument Noise,

J. Chem. Phys. 129, 024102.1-024102.8 (2008).

by P. Maragakis, F. Ritort, C. Bustamante, M. Karplus, and G. E. Crooks.

 

774.  A Differential Fluctuation Theorem,

J. Phys. Chem. B 112, 6168-6174 (2008),

by P. L. Maragakis, M. Spichty, and M. Karplus.

 

775.  Allostery and Cooperativity Revisited,

Protein Science 17, 1295-1307 (2008),

by Q. Cui and M. Karplus.

 

776.  Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements,

PLoS Computational Biology 4, e1000129:1-19 (2008),

by M. Cecchini, A. Houdusse, and M. Karplus.

 

777.  One-Dimensional Barrier Preserving Free-Energy Projections of a b‑sheet Miniprotein:

New Insights into the Folding Process,

J. Phys. Chem. B 112, 8701-8714 (2008),

by S. Krivov, S. Muff, A. Caflisch, and M. Karplus.

 

778.  Diffusive Reaction Dynamics on Invariant Free Energy,

Proc. Natl. Acad. Sci. USA 105, 13841-13846 (2008),

by S. Krivov and M. Karplus.

 

779.  The Human Cytomegalovirus UL44 C Clamp Wraps Around DNA,

Structure 16, 1214-1225 (2008),

by G. Komazin-Meredith, R. J. Petrella, W. L. Santos, C. G. Gartner, D. J. Filman, J. M. Hogle, G. L. Verdine, M. Karplus, and D. M. Coen.

 

780.  Kinesin's Cover-Neck Bundle Folds Forward to Generate Force,

Proc. Natl. Acad. Sci. USA 105, 19246-19251 (2008),

by A. S. Khalil, D. C. Appleyard, A. K. Labno, A. Georges, M. Karplus, A. M. Belcher, W. Hwang, M. J. Lang.

 

781.  Signaling Pathways of the PDZ2 Domain: A Molecular Dynamnics Interaction Correlation

Analysis,

Proteins: Structure, Function & Genetics 74, 145-154 (2009),

by Y. Kong and M. Karplus.

 

Books:  

 

M. Karplus and R. N. Porter, Atoms & Molecules: An Introduction for Students of Physical Chemistry (Benjamin, 1970).

 

C. L. Brooks III, M. Karplus, and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure, & Thermodynamics, Adv. Chem. Phys. LXXI (John Wiley & Sons, 1988).

 

O. M. Becker and M. Karplus, A Guide to Biomolecular Simulations (Springer, 2006).