Publications of V. Gapsys

Journal Article (31)

21.
Journal Article
Matthes, D.; Gapsys, V.; Brennecke, J. T.; de Groot, B. L.: An atomistic view of amyloidogenic self-assembly: Structure and dynamics of heterogeneous conformational states in the pre-nucleation phase. Scientific Reports 6, 33156 (2016)
22.
Journal Article
Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angewandte Chemie-International Edition 55 (26), pp. 7364 - 7368 (2016)
23.
Journal Article
Rauscher, S.; Gapsys, V.; Gajda, M. J.; Zweckstetter, M.; de Groot, B. L.; Grubmüller, H.: Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation 11 (11), pp. 5513 - 5524 (2015)
24.
Journal Article
Gapsys, V.; Narayanan, R. L.; Xiang, S.; de Groot, B. L.; Zweckstetter, M.: Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 63 (3), pp. 299 - 307 (2015)
25.
Journal Article
Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 36 (5), pp. 348 - 354 (2015)
26.
Journal Article
Xiang, S. Q.; Gapsys, V.; Kim, H. Y.; Bessonov, S.; Hsiao, H. H.; Möhlmann, S.; Klaukien, V.; Ficner, R.; Becker, S.; Urlaub, H. et al.; Lührmann, R.; de Groot, B.; Zweckstetter, M.: Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 21 (12), pp. 2162 - 2174 (2013)
27.
Journal Article
Gapsys, V.; de Groot, B. L.; Briones, R.: Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 27 (10), pp. 845 - 858 (2013)
28.
Journal Article
Gapsys, V.; de Groot, B. L.: Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), pp. 196 - 207 (2013)
29.
Journal Article
Matthes, D.; Gapsys, V.; de Groot, B. L.: Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. Journal of Molecular Biology 421 (2-3), pp. 390 - 416 (2012)
30.
Journal Article
Gapsys, V.; Seeliger, D.; de Groot, B. L.: New soft-core potential function for molecular dynamics based alchemical free energy calculations. Journal of Chemical Theory and Computation 8 (7), pp. 2373 - 2382 (2012)
31.
Journal Article
Matthes, D.; Gapsys, V.; Daebel, V.; de Groot, B. L.: Mapping the conformational dynamics and pathways of spontaneous steric zipper peptide oligomerization. Plos One 6 (5), e19129 (2011)

Book Chapter (2)

32.
Book Chapter
Aldeghi, M.; de Groot, B. L.; Gapsys, V.: 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)
33.
Book Chapter
Gapsys, V.; Michielssens, S.; Peters, J. H.; de Groot, B.; Leonov, H.: 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)

34.
Conference Paper
Gapsys, V.; de Groot, B.: 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 114 (3, Suppl. 1), p. 674a - 674a (2018)
35.
Conference Paper
Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L.: 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 110 (Suppl 1), 3 Ed., p. 368A - 368A (2016)
36.
Conference Paper
Rauscher, S.; Gapsys, V.; Zhou, M.; Van, Q.; Gajda, M. J.; Zweckstetter, M.; Enderlein, J.; de Groot, B. L.; Grubmüller, H.: 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 110 (Suppl 1), 3 Ed., p. 358A - 358A (2016)
37.
Conference Paper
Rauscher, S.; Gapsys, V.; de Groot, B. L.; Grubmüller, H.; H: Structural ensembles of intrinsically disordered proteins using molecular dynamics simulation. Biophysical Journal 108 (Supplement 1), p. 14A - 14A (2015)
38.
Conference Paper
Gapsys, V.; de Groot, B.: Computational thrombin inhibitor optimization. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, February 15, 2014 - February 19, 2014. Biophysical Journal 106 (Suppl. 1), 2 Ed., pp. 262a - 263a (2014)
39.
Conference Paper
Rauscher, S.; Gapsys, V.; Volkhardt, A.; Blau, C.; de Groot, B. L.; Grubmüller, H.: 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 106 (2, Suppl. 1), p. 271a (2014)

Thesis - PhD (1)

40.
Thesis - PhD
Gapsys, V.: Free energy calculations for protein-ligand comlexes and intrinsically disordered peptides and their aggregates. Dissertation, Georg-August-Universität, Göttingen (2013)
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