vytautas gapsys
vytautas gapsys
Senior Scientist at Janssen (Johnson & Johnson). Previously, project leader at Max Planck Institute
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Zitiert von
Zitiert von
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
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
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
Computational analysis of local membrane properties
V Gapsys, BL de Groot, R Briones
Journal of computer-aided molecular design 27, 845-858, 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
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
Calculation of binding free energies
V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov
Molecular Modeling of Proteins, 173-209, 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
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
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
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
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
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
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
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
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
pmx Webserver: a user friendly interface for alchemistry
V Gapsys, BL de Groot
Journal of chemical information and modeling 57 (2), 109-114, 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
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
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
V Gapsys, BL de Groot
Elife 9, e57589, 2020
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