| 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 | 323 | 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 | 118 | 2015 |
| Computational analysis of local membrane properties V Gapsys, BL de Groot, R Briones Journal of computer-aided molecular design 27 (10), 845-858, 2013 | 116 | 2013 |
| 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 | 91 | 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 | 81 | 2016 |
| 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 | 78 | 2012 |
| 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 | 70 | 2012 |
| Calculation of binding free energies V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov Molecular Modeling of Proteins, 173-209, 2015 | 55 | 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 | 53 | 2020 |
| 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 | 53 | 2016 |
| 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 | 51 | 2011 |
| 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 | 49 | 2020 |
| 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 | 42 | 2018 |
| pmx Webserver: a user friendly interface for alchemistry V Gapsys, BL de Groot Journal of chemical information and modeling 57 (2), 109-114, 2017 | 29 | 2017 |
| Optimal superpositioning of flexible molecule ensembles V Gapsys, BL de Groot Biophysical journal 104 (1), 196-207, 2013 | 24 | 2013 |
| Alchemical free energy calculations for nucleotide mutations in protein–DNA complexes V Gapsys, BL de Groot Journal of chemical theory and computation 13 (12), 6275-6289, 2017 | 23 | 2017 |
| Comment on'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size' V Gapsys, BL de Groot Elife 8, e44718, 2019 | 22 | 2019 |
| An atomistic view of amyloidogenic self-assembly: structure and dynamics of heterogeneous conformational states in the pre-nucleation phase D Matthes, V Gapsys, JT Brennecke, BL de Groot Scientific reports 6 (1), 1-19, 2016 | 21 | 2016 |
| Predicting kinase inhibitor resistance: physics-based and data-driven approaches M Aldeghi, V Gapsys, BL de Groot ACS central science 5 (8), 1468-1474, 2019 | 18 | 2019 |
| Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes” V Gapsys, M Khabiri, BL de Groot, PL Freddolino The Journal of Physical Chemistry B 124 (6), 1115-1123, 2018 | 17 | 2018 |
Bert L. de GrootMax Planck Institute for biophysical chemistryVerified email at gwdg.de
