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
2732015
Computational analysis of local membrane properties
V Gapsys, BL de Groot, R Briones
Journal of computer-aided molecular design 27 (10), 845-858, 2013
912013
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
852015
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
802013
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
662012
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
642016
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
632012
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
442016
Calculation of binding free energies
V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov
Molecular Modeling of Proteins, 173-209, 2015
432015
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
242018
Optimal superpositioning of flexible molecule ensembles
V Gapsys, BL de Groot
Biophysical journal 104 (1), 196-207, 2013
232013
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
202020
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
202020
pmx Webserver: a user friendly interface for alchemistry
V Gapsys, BL de Groot
Journal of chemical information and modeling 57 (2), 109-114, 2017
202017
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
162017
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
162016
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
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
102018
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
92019
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Articles 1–20