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vytautas gapsys
vytautas gapsys
Senior Scientist at Janssen (Johnson & Johnson). Previously, project Leader at Max Planck Institute
Verified email at gwdg.de - Homepage
Title
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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
3442015
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
1612015
Computational analysis of local membrane properties
V Gapsys, BL de Groot, R Briones
Journal of computer-aided molecular design 27 (10), 845-858, 2013
1342013
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
1022016
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
1012020
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
982013
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
862012
Calculation of binding free energies
V Gapsys, S Michielssens, JH Peters, BL Groot, H Leonov
Molecular Modeling of Proteins, 173-209, 2015
832015
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
782020
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
722012
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
632018
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
622016
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
522011
pmx Webserver: a user friendly interface for alchemistry
V Gapsys, BL de Groot
Journal of chemical information and modeling 57 (2), 109-114, 2017
412017
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
302019
Comment on'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
V Gapsys, BL de Groot
Elife 8, 2019
292019
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
272017
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
252016
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), 1-13, 2021
242021
Optimal superpositioning of flexible molecule ensembles
V Gapsys, BL de Groot
Biophysical journal 104 (1), 196-207, 2013
242013
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Articles 1–20