| Structural ensembles of intrinsically disordered proteins depend strongly on force field: a comparison to experiment S Rauscher, V Gapsys, MJ Gajda, M Zweckstetter, BL De Groot, ... Journal of chemical theory and computation 11 (11), 5513-5524, 2015 | 424 | 2015 |
| pmx: Automated protein structure and topology generation for alchemical perturbations V Gapsys, S Michielssens, D Seeliger, BL De Groot Journal of computational chemistry 36 (5), 348-354, 2015 | 238 | 2015 |
| Large scale relative protein ligand binding affinities using non-equilibrium alchemy V Gapsys, L Pérez-Benito, M Aldeghi, D Seeliger, H Van Vlijmen, ... Chemical Science 11 (4), 1140-1152, 2020 | 202 | 2020 |
| Computational analysis of local membrane properties V Gapsys, BL de Groot, R Briones Journal of computer-aided molecular design 27, 845-858, 2013 | 164 | 2013 |
| Accurate and rigorous prediction of the changes in protein free energies in a large‐scale mutation scan V Gapsys, S Michielssens, D Seeliger, BL de Groot Angewandte Chemie International Edition 55 (26), 7364-7368, 2016 | 134 | 2016 |
| Phosphorylation drives a dynamic switch in serine/arginine-rich proteins SQ Xiang, V Gapsys, HY Kim, S Bessonov, HH Hsiao, S Möhlmann, ... Structure 21 (12), 2162-2174, 2013 | 122 | 2013 |
| Calculation of binding free energies V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov Molecular Modeling of Proteins, 173-209, 2015 | 117 | 2015 |
| The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations A Rizzi, T Jensen, DR Slochower, M Aldeghi, V Gapsys, D Ntekoumes, ... Journal of computer-aided molecular design 34 (5), 601-633, 2020 | 114 | 2020 |
| New soft-core potential function for molecular dynamics based alchemical free energy calculations V Gapsys, D Seeliger, BL de Groot Journal of chemical theory and computation 8 (7), 2373-2382, 2012 | 109 | 2012 |
| Accurate estimation of ligand binding affinity changes upon protein mutation M Aldeghi, V Gapsys, BL de Groot ACS central science 4 (12), 1708-1718, 2018 | 95 | 2018 |
| Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC H Ilgü, JM Jeckelmann, V Gapsys, Z Ucurum, BL de Groot, D Fotiadis Proceedings of the National Academy of Sciences 113 (37), 10358-10363, 2016 | 80 | 2016 |
| Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations D Matthes, V Gapsys, BL de Groot Journal of molecular biology 421 (2-3), 390-416, 2012 | 80 | 2012 |
| Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field S Boothroyd, PK Behara, OC Madin, DF Hahn, H Jang, V Gapsys, ... Journal of chemical theory and computation 19 (11), 3251-3275, 2023 | 78 | 2023 |
| Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches V Gapsys, A Yildirim, M Aldeghi, Y Khalak, D Van der Spoel, BL de Groot Communications Chemistry 4 (1), 61, 2021 | 72 | 2021 |
| GROMACS in the cloud: A global supercomputer to speed up alchemical drug design C Kutzner, C Kniep, A Cherian, L Nordstrom, H Grubmüller, BL de Groot, ... Journal of Chemical Information and Modeling 62 (7), 1691-1711, 2022 | 62 | 2022 |
| Alchemical absolute protein–ligand binding free energies for drug design Y Khalak, G Tresadern, M Aldeghi, HM Baumann, DL Mobley, ... Chemical science 12 (41), 13958-13971, 2021 | 60 | 2021 |
| pmx Webserver: a user friendly interface for alchemistry V Gapsys, BL de Groot Journal of chemical information and modeling 57 (2), 109-114, 2017 | 58 | 2017 |
| Mapping the conformational dynamics and pathways of spontaneous steric zipper peptide oligomerization D Matthes, V Gapsys, V Daebel, BL de Groot PloS one 6 (5), e19129, 2011 | 55 | 2011 |
| Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [article v1. 0] DF Hahn, CI Bayly, ML Boby, HEB Macdonald, JD Chodera, V Gapsys, ... Living journal of computational molecular science 4 (1), 2022 | 54 | 2022 |
| On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size V Gapsys, BL de Groot Elife 9, e57589, 2020 | 53 | 2020 |
Bert L. de GrootMax Planck Institute for multidisciplinary sciencesVerified email at gwdg.de
