vytautas gapsys
vytautas gapsys
Max Planck Institute for Biophysical Chemistry, Goettingen
Verifierad e-postadress på gwdg.de
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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
2612015
Computational analysis of local membrane properties
V Gapsys, BL de Groot, R Briones
Journal of computer-aided molecular design 27 (10), 845-858, 2013
872013
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
772013
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
722015
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
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
612012
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
592016
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
452011
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
412016
Calculation of binding free energies
V Gapsys, S Michielssens, JH Peters, BL de Groot, H Leonov
Molecular Modeling of Proteins, 173-209, 2015
392015
Optimal superpositioning of flexible molecule ensembles
V Gapsys, BL de Groot
Biophysical journal 104 (1), 196-207, 2013
232013
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
202018
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
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
152017
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
142020
pmx Webserver: a user friendly interface for alchemistry
V Gapsys, BL de Groot
Journal of chemical information and modeling 57 (2), 109-114, 2017
142017
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
132017
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
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
82020
Comment on'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
V Gapsys, BL de Groot
Elife 8, e44718, 2019
72019
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Artiklar 1–20