Publications of V. Gapsys

Gapsys, V.; de Groot, B. L.: Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), pp. 196 - 207 (2013)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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