Publications of V. Gapsys
All genres
Journal Article (42)
21.
Journal Article
33, pp. 1031 - 1043 (2019)
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 22.
Journal Article
5 (8), pp. 1468 - 1474 (2019)
Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 23.
Journal Article
8, e44718 (2019)
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 24.
Journal Article
40 (6), pp. 816 - 827 (2019)
Pyruvate carboxylase deficiency type A and type C: Characterization of 5 novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human Mutation 25.
Journal Article
4 (12), pp. 1708 - 1718 (2018)
Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 26.
Journal Article
14 (7), pp. 3397 - 3408 (2018)
Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 27.
Journal Article
138-139, pp. 85 - 92 (2018)
Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 28.
Journal Article
8 (12), pp. 2791 - 2808 (2017)
Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience 29.
Journal Article
13 (12), pp. 6275 - 6289 (2017)
Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. Journal of Chemical Theory and Computation 30.
Journal Article
57 (2), pp. 109 - 114 (2017)
pmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling 31.
Journal Article
113 (37), pp. 10358 - 10363 (2016)
Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proceedings of the National Academy of Sciences of the United States of America 32.
Journal Article
6, 33156 (2016)
An atomistic view of amyloidogenic self-assembly: Structure and dynamics of heterogeneous conformational states in the pre-nucleation phase. Scientific Reports 33.
Journal Article
55 (26), pp. 7364 - 7368 (2016)
Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angewandte Chemie-International Edition 34.
Journal Article
11 (11), pp. 5513 - 5524 (2015)
Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation 35.
Journal Article
63 (3), pp. 299 - 307 (2015)
Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 36.
Journal Article
36 (5), pp. 348 - 354 (2015)
Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 37.
Journal Article
21 (12), pp. 2162 - 2174 (2013)
Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 38.
Journal Article
27 (10), pp. 845 - 858 (2013)
Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 39.
Journal Article
104 (1), pp. 196 - 207 (2013)
Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 40.
Journal Article
421 (2-3), pp. 390 - 416 (2012)
Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. Journal of Molecular Biology