vytautas gapsys
vytautas gapsys
Project Leader at Max Planck Institute for Biophysical Chemistry, Goettingen
Verified email at gwdg.de
Cited by
Cited by
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
Computational analysis of local membrane properties
V Gapsys, BL de Groot, R Briones
Journal of computer-aided molecular design 27 (10), 845-858, 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
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
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
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
Calculation of binding free energies
V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov
Molecular Modeling of Proteins, 173-209, 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
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
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
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
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
pmx Webserver: a user friendly interface for alchemistry
V Gapsys, BL de Groot
Journal of chemical information and modeling 57 (2), 109-114, 2017
Optimal superpositioning of flexible molecule ensembles
V Gapsys, BL de Groot
Biophysical journal 104 (1), 196-207, 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
Comment on'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
V Gapsys, BL de Groot
Elife 8, e44718, 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
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
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
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