(Q33713877)

28 July 2017

title

Simulation of the folding equilibrium of alpha-helical peptides: a comparison of the generalized Born approximation with explicit solvent (English)

1 reference

28 July 2017

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent (English)

1 reference

DOI

https://api.crossref.org/works/10.1073/PNAS.2232868100

2 April 2024

Angel E García

1 reference

28 July 2017

Hugh Nymeyer

1 reference

28 July 2017

language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=14617775

2 April 2024

publication date

14 November 2003

1 reference

full work available at URL

28 July 2017

https://europepmc.org/articles/pmc283524?pdf=render

file format

Portable Document Format

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14617775

https://europepmc.org/articles/PMC283524

2 April 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14617775

https://europepmc.org/articles/PMC283524?pdf=render

2 April 2024

file format

Portable Document Format

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14617775

https://doi.org/10.1073/pnas.2232868100

2 April 2024

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A14617775

https://pnas.org/doi/pdf/10.1073/pnas.2232868100

2 April 2024

1 reference

DOI

https://api.crossref.org/works/10.1073/PNAS.2232868100

Proceedings of the National Academy of Sciences of the United States of America

2 April 2024

published in

1 reference

28 July 2017

volume

100

1 reference

28 July 2017

1 reference

28 July 2017

page(s)

13934-13939

1 reference

Folding of a highly conserved diverging turn motif from the SH3 domain

28 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Surfing on protein folding energy landscapes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Absolute comparison of simulated and experimental protein-folding dynamics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

14 July 2018

1 reference

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Native-like mean structure in the unfolded ensemble of small proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Effective Born radii in the generalized Born approximation: the importance of being perfect

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

The enthalpy of the alanine peptide helix measured by isothermal titration calorimetry using metal-binding to induce helix formation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

The free energy landscape for beta hairpin folding in explicit water

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the C' position of the C-capping box of alpha-helices

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Generalized born models of macromolecular solvation effects

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Effective energy function for proteins in solution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Conformation in solution and dynamics of a structurally constrained linear insect kinin pentapeptide analogue

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Canonical dynamics: Equilibrium phase-space distributions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Folding dynamics and mechanism of beta-hairpin formation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Fast events in protein folding: helix melting and formation in a small peptide.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Electrostatic screening of charge and dipole interactions with the helix backbone

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Solvation energy in protein folding and binding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

The mechanism of alpha-helix formation by peptides

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Semianalytical treatment of solvation for molecular mechanics and dynamics

14 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

MEARA sequence repeat of human CstF-64 polyadenylation factor is helical in solution. A spectroscopic and calorimetric study.

21 January 2018

1 reference

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Comparison of simple potential functions for simulating liquid water

21 January 2018

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

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Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains

21 January 2018

1 reference

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Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Evaluation of Models of Electrostatic Interactions in Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

pKaShifts in Small Molecules and HIV Protease: Electrostatics and Conformation

21 January 2018

1 reference

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Protein molecular dynamics with the generalized born/ACE solvent model

21 January 2018

2 references

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

21 January 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Continuum solvent molecular dynamics study of flexibility in interleukin-8

30 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Helix-coil transitions re-visited

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=283524

Ion pair potentials-of-mean-force in water

30 October 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Computer simulation of aqueous Na-Cl electrolytes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.2232868100

Exploring the energy landscape of a beta hairpin in explicit solvent

21 January 2018

1 reference

12 December 2020

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Prediction of loop geometries using a generalized born model of solvation effects

1 reference

12 December 2020

Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution

1 reference

https://api.crossref.org/works/10.1073/PNAS.2232868100

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules

2 April 2024

1 reference

https://api.crossref.org/works/10.1073/PNAS.2232868100

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

2 April 2024

1 reference

https://api.crossref.org/works/10.1073/PNAS.2232868100

2 April 2024

Identifiers

DOI

1 reference

28 July 2017

0 references

1 reference

28 July 2017

1 reference