vytautas gapsys
vytautas gapsys
Project Leader at Max Planck Institute for Biophysical Chemistry, Goettingen
Verified email at gwdg.de
Title
Cited by
Cited by
Year
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
2842015
Computational analysis of local membrane properties
V Gapsys, BL de Groot, R Briones
Journal of computer-aided molecular design 27 (10), 845-858, 2013
952013
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
902015
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
812013
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
682016
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
682012
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
652012
Calculation of binding free energies
V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov
Molecular Modeling of Proteins, 173-209, 2015
512015
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
472011
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
462016
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
302018
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, 1-33, 2020
272020
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
272020
Optimal superpositioning of flexible molecule ensembles
V Gapsys, BL de Groot
Biophysical journal 104 (1), 196-207, 2013
232013
pmx Webserver: a user friendly interface for alchemistry
V Gapsys, BL de Groot
Journal of chemical information and modeling 57 (2), 109-114, 2017
222017
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
182017
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, 33156, 2016
172016
Resolving the atomistic modes of Anle138b inhibitory action on peptide oligomer formation
D Matthes, V Gapsys, C Griesinger, BL de Groot
ACS chemical neuroscience 8 (12), 2791-2808, 2017
142017
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
112019
Comment on'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
V Gapsys, BL de Groot
Elife 8, e44718, 2019
112019
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Articles 1–20