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2020 – today
- 2024
[j44]Gregory A. Landrum
, Sereina Riniker:
Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise. J. Chem. Inf. Model. 64(5): 1560-1567 (2024)- [j43]Gregory A. Landrum, Jessica Braun, Paul Katzberger, Marc Lehner, Sereina Riniker:
lwreg: A Lightweight System for Chemical Registration and Data Storage. J. Chem. Inf. Model. 64(16): 6247-6252 (2024) - [j42]Jessica Braun, Paul Katzberger, Gregory A. Landrum, Sereina Riniker:
Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings. J. Chem. Inf. Model. 64(20): 7917-7924 (2024) - [j41]Franz Waibl, Fabio Casagrande, Fabian Dey, Sereina Riniker:
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents. J. Chem. Inf. Model. 64(20): 7938-7948 (2024) - 2023
- [j40]Salomé Rieder, Marina P. Oliveira, Sereina Riniker, Philippe H. Hünenberger:
Development of an open-source software for isomer enumeration. J. Cheminformatics 15(1): 10 (2023) - [j39]Gregory A. Landrum, Maximilian Beckers, Jessica Lanini, Nadine Schneider, Nikolaus Stiefl, Sereina Riniker:
SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches. J. Cheminformatics 15(1): 119 (2023) - [j38]Emília P. Barros, Benjamin Ries, Candide Champion, Salomé Rieder, Sereina Riniker:
Accounting for Solvation Correlation Effects on the Thermodynamics of Water Networks in Protein Cavities. J. Chem. Inf. Model. 63(6): 1794-1805 (2023) - [j37]Patrick Bleiziffer, Kay Schaller, Sereina Riniker:
Correction to "Machine Learning of Partial Charges Derived From High-Quality Quantum-Mechanical Calculations". J. Chem. Inf. Model. 63(7): 2265 (2023) - [j36]Marc Lehner, Paul Katzberger, Niels Maeder, Carl C. G. Schiebroek, Jakob Teetz, Gregory A. Landrum, Sereina Riniker:
DASH: Dynamic Attention-Based Substructure Hierarchy for Partial Charge Assignment. J. Chem. Inf. Model. 63(19): 6014-6028 (2023) - [j35]Candide Champion, René Gall, Benjamin Ries, Salomé Rieder, Emília P. Barros, Sereina Riniker:
Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases. J. Chem. Inf. Model. 63(22): 7133-7147 (2023) - [c1]Moritz Thürlemann, Sereina Riniker:
Anisotropic Message Passing: Graph Neural Networks with Directional and Long-Range Interactions. ICLR 2023 - 2022
- [j34]Benjamin Ries, Karl Normak, R. Gregor Weiß, Salomé Rieder, Emília P. Barros, Candide Champion, Gerhard König, Sereina Riniker:
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure. J. Comput. Aided Mol. Des. 36(2): 117-130 (2022) - [j33]Benjamin Ries, Salomé Rieder, Clemens Rhiner, Philippe H. Hünenberger, Sereina Riniker:
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology. J. Comput. Aided Mol. Des. 36(3): 175-192 (2022) - [j32]Shuzhe Wang, Kajo Krummenacher, Gregory A. Landrum, Benjamin D. Sellers, Paola Di Lello, Sarah J. Robinson, Bryan Martin, Jeffrey K. Holden, Jeffrey Y. K. Tom, Anastasia C. Murthy, Nataliya Popovych, Sereina Riniker:
Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry. J. Chem. Inf. Model. 62(3): 472-485 (2022) - [j31]Salomé Rieder, Benjamin Ries, Kay Schaller, Candide Champion, Emília P. Barros, Philippe H. Hünenberger, Sereina Riniker:
Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules. J. Chem. Inf. Model. 62(12): 3043-3056 (2022) - 2021
- [j30]Benjamin Ries, Stephanie M. Linker, David F. Hahn, Gerhard König, Sereina Riniker:
Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations. J. Chem. Inf. Model. 61(2): 560-564 (2021) - [j29]Mahendra Awale, Jérôme Hert, Laura Guasch, Sereina Riniker, Christian Kramer:
The Playbooks of Medicinal Chemistry Design Moves. J. Chem. Inf. Model. 61(2): 729-742 (2021) - [j28]Carmen Esposito, Gregory A. Landrum, Nadine Schneider, Nikolaus Stiefl, Sereina Riniker:
GHOST: Adjusting the Decision Threshold to Handle Imbalanced Data in Machine Learning. J. Chem. Inf. Model. 61(6): 2623-2640 (2021) - 2020
- [j27]Shuzhe Wang, Sereina Riniker:
Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge. J. Comput. Aided Mol. Des. 34(4): 393-403 (2020) - [j26]Kira A. Armacost, Sereina Riniker, Zoe Cournia:
Novel Directions in Free Energy Methods and Applications. J. Chem. Inf. Model. 60(1): 1-5 (2020) - [j25]Shuzhe Wang, Jagna Witek, Gregory A. Landrum, Sereina Riniker:
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences. J. Chem. Inf. Model. 60(4): 2044-2058 (2020) - [j24]Mahendra Awale, Sereina Riniker, Christian Kramer:
Matched Molecular Series Analysis for ADME Property Prediction. J. Chem. Inf. Model. 60(6): 2903-2914 (2020) - [j23]Carmen Esposito, Shuzhe Wang, Udo E. W. Lange, Frank Oellien, Sereina Riniker:
Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. J. Chem. Inf. Model. 60(10): 4730-4749 (2020) - [j22]Kira A. Armacost, Sereina Riniker, Zoe Cournia:
Exploring Novel Directions in Free Energy Calculations. J. Chem. Inf. Model. 60(11): 5283-5286 (2020) - [j21]Julia Gebhardt, Matthias Kiesel, Sereina Riniker, Niels Hansen:
Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients. J. Chem. Inf. Model. 60(11): 5319-5330 (2020) - [j20]Gerhard König, Nina Glaser, Benjamin Schroeder, Alzbeta Kubincová, Philippe H. Hünenberger, Sereina Riniker:
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling. J. Chem. Inf. Model. 60(11): 5407-5423 (2020)
2010 – 2019
- 2019
- [j19]Jagna Witek, Shuzhe Wang, Benjamin Schroeder, Robin Lingwood, Andreas Dounas, Hans-Jörg Roth, Marianne Fouché, Markus Blatter, Oliver Lemke, Bettina G. Keller, Sereina Riniker:
Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model. 59(1): 294-308 (2019) - [j18]Lennard Böselt, Dominik Sidler, Tobias Kittelmann, Jürgen Stohner, Daniel Zindel, Trixie Wagner, Sereina Riniker:
Determination of Absolute Stereochemistry of Flexible Molecules Using a Vibrational Circular Dichroism Spectra Alignment Algorithm. J. Chem. Inf. Model. 59(5): 1826-1838 (2019) - 2018
- [j17]Sereina Riniker:
Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. J. Chem. Inf. Model. 58(3): 565-578 (2018) - [j16]Patrick Bleiziffer, Kay Schaller, Sereina Riniker:
Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations. J. Chem. Inf. Model. 58(3): 579-590 (2018) - [j15]Andrea Volkamer, Sereina Riniker:
Transition from Academia to Industry and Back. J. Chem. Inf. Model. 58(8): 1469-1472 (2018) - [i1]Dominik Sidler, Marc Lehner, Simon Frasch, Michael Cristófol-Clough, Sereina Riniker:
Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations. F1000Research 7: 1745 (2018) - 2017
- [j14]Sereina Riniker:
Molecular Dynamics Fingerprints (MDFP): Machine Learning from MD Data To Predict Free-Energy Differences. J. Chem. Inf. Model. 57(4): 726-741 (2017) - [j13]Jagna Witek, Bettina G. Keller, Markus Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker:
Correction to Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. 57(9): 2393 (2017) - 2016
- [j12]Jagna Witek, Bettina G. Keller, Marie-Claude Blatter, Axel Meissner, Trixie Wagner, Sereina Riniker:
Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J. Chem. Inf. Model. 56(8): 1547-1562 (2016) - 2015
- [j11]Sereina Riniker, Gregory A. Landrum:
Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation. J. Chem. Inf. Model. 55(12): 2562-2574 (2015) - 2014
- [j10]Charleen G. Don, Sereina Riniker:
Scents and sense: In silico perspectives on olfactory receptors. J. Comput. Chem. 35(32): 2279-2287 (2014) - [j9]Sereina Riniker, Yuan Wang, Jeremy L. Jenkins, Gregory A. Landrum:
Using Information from Historical High-Throughput Screens to Predict Active Compounds. J. Chem. Inf. Model. 54(7): 1880-1891 (2014) - 2013
- [j8]Sereina Riniker, Gregory A. Landrum:
Open-source platform to benchmark fingerprints for ligand-based virtual screening. J. Cheminformatics 5: 26 (2013) - [j7]Sereina Riniker, Gregory A. Landrum:
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. J. Cheminformatics 5: 43 (2013) - [j6]Sereina Riniker, Nikolas Fechner, Gregory A. Landrum:
Heterogeneous Classifier Fusion for Ligand-Based Virtual Screening: Or, How Decision Making by Committee Can Be a Good Thing. J. Chem. Inf. Model. 53(11): 2829-2836 (2013) - 2012
- [j5]Sereina Riniker, Luzi J. Barandun, François Diederich, Oliver Krämer, Andreas Steffen, Wilfred F. van Gunsteren:
Free enthalpies of replacing water molecules in protein binding pockets. J. Comput. Aided Mol. Des. 26(12): 1293-1309 (2012) - [j4]Anna-Pitschna E. Kunz, Jane R. Allison, Daan P. Geerke, Bruno A. C. Horta, Philippe H. Hünenberger, Sereina Riniker, Nathan Schmid, Wilfred F. van Gunsteren:
New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 33(3): 340-353 (2012) - [j3]Niels Hansen, Jozica Dolenc, Matthias Knecht, Sereina Riniker, Wilfred F. van Gunsteren:
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. J. Comput. Chem. 33(6): 640-651 (2012) - [j2]Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren, Philippe H. Hünenberger:
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. J. Comput. Chem. 33(24): 1907-1917 (2012) - 2011
- [j1]Jozica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura, Wilfred F. van Gunsteren:
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. J. Comput. Aided Mol. Des. 25(8): 709-716 (2011)
Coauthor Index
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