Publications of V. Gapsys
All genres
Journal Article (32)
21.
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 22.
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 23.
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 24.
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 25.
Journal Article
63 (3), pp. 299 - 307 (2015)
Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 26.
Journal Article
36 (5), pp. 348 - 354 (2015)
Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 27.
Journal Article
21 (12), pp. 2162 - 2174 (2013)
Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 28.
Journal Article
27 (10), pp. 845 - 858 (2013)
Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 29.
Journal Article
104 (1), pp. 196 - 207 (2013)
Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 30.
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 31.
Journal Article
8 (7), pp. 2373 - 2382 (2012)
New soft-core potential function for molecular dynamics based alchemical free energy calculations. Journal of Chemical Theory and Computation 32.
Journal Article
6 (5), e19129 (2011)
Mapping the conformational dynamics and pathways of spontaneous steric zipper peptide oligomerization. Plos One Book Chapter (2)
33.
Book Chapter
Accurate calculation of free energy changes upon amino acid mutation. In: Computational Methods in Protein Evolution, pp. 19 - 47 (Ed. Sikosek, T.). Springer Nature, New York (2019)
34.
Book Chapter
Calculation of binding free energies. In: Molecular Modeling of Proteins, pp. 173 - 209 (Ed. Kukol, A.). Humana Pr.; Springer, New York, N.Y. (2015)
Conference Paper (6)
35.
Conference Paper
114 (3, Suppl. 1), p. 674a - 674a (2018)
A unified framework for alchemical mutations in proteins, DNA and ligands. 62nd Annual Meeting of the Biophysical-Society, San Francisco, CA, February 17, 2018 - February 21, 2018. Biophysical Journal 36.
Conference Paper
110 (Suppl 1), 3 Ed., p. 368A - 368A (2016)
Insights from the first Principles based large scale protein thermostability calculations. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, February 27, 2016 - March 02, 2016. Biophysical Journal 37.
Conference Paper
110 (Suppl 1), 3 Ed., p. 358A - 358A (2016)
Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, February 27, 2016 - March 02, 2016. Biophysical Journal 38.
Conference Paper
108 (Supplement 1), p. 14A - 14A (2015)
Structural ensembles of intrinsically disordered proteins using molecular dynamics simulation. Biophysical Journal 39.
Conference Paper
106 (Suppl. 1), 2 Ed., pp. 262a - 263a (2014)
Computational thrombin inhibitor optimization. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, February 15, 2014 - February 19, 2014. Biophysical Journal 40.
Conference Paper
106 (2, Suppl. 1), p. 271a (2014)
Structural ensembles of intrinsically disordered proteins depend strongly on force field. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, February 15, 2014 - February 19, 2014. Biophysical Journal