Vytautas Gapsys

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  • 2022 | Journal Article | Research Paper
    ​ ​Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case​
    Wieczór, M.; Genna, V.; Aranda, J.; Badia, R. M.; Gelpí, J. L.; Gapsys, V.   & de Groot, B. L.  et al.​ (2022) 
    Wiley Interdisciplinary Reviews. Computational Molecular Science,.​ DOI: https://doi.org/10.1002/wcms.1622 
    ​Details  DOI 
  • 2022 | Journal Article | 
    ​ ​A litmus test for classifying recognition mechanisms of transiently binding proteins​
    Chakrabarti, K. S.; Olsson, S.; Pratihar, S. ; Giller, K. ; Overkamp, K.; Lee, K. O. & Gapsys, V.  et al.​ (2022) 
    Nature Communications, 13(1).​ DOI: https://doi.org/10.1038/s41467-022-31374-5 
    ​Details  DOI 
  • 2022 | Journal Article | 
    ​ ​Chemical Space Exploration with Active Learning and Alchemical Free Energies​
    Khalak, Y.; Tresadern, G.; Hahn, D. F.; de Groot, B. L.   & Gapsys, V. ​ (2022) 
    Journal of Chemical Theory and Computation, art. acs.jctc.2c00752​.​ DOI: https://doi.org/10.1021/acs.jctc.2c00752 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes”​
    Gapsys, V. ; Khabiri, M.; de Groot, B. L.   & Freddolino, P. L.​ (2020) 
    The Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 124(6) pp. 1115​-1123​.​ DOI: https://doi.org/10.1021/acs.jpcb.8b04187 
    ​Details  DOI 
  • 2020 | Journal Article
    ​ ​The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations​
    Rizzi, A.; Jensen, T.; Slochower, D. R.; Aldeghi, M.; Gapsys, V. ; Ntekoumes, D. & Bosisio, S. et al.​ (2020) 
    Journal of Computer-Aided Molecular Design, 34(5) pp. 601​-633​.​ DOI: https://doi.org/10.1007/s10822-020-00290-5 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Large scale relative protein ligand binding affinities using non-equilibrium alchemy​
    Gapsys, V. ; Pérez-Benito, L.; Aldeghi, M.; Seeliger, D.; van Vlijmen, H.; Tresadern, G. & de Groot, B. L. ​ (2020) 
    Chemical Science, 11(4) pp. 1140​-1152​.​ DOI: https://doi.org/10.1039/C9SC03754C 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size​
    Gapsys, V.   & de Groot, B. L. ​ (2020) 
    eLife, 9.​ DOI: https://doi.org/10.7554/eLife.57589 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors​
    Bastys, T.; Gapsys, V. ; Walter, H.; Heger, E.; Doncheva, N. T.; Kaiser, R. & de Groot, B. L.  et al.​ (2020) 
    Retrovirology, 17(1).​ DOI: https://doi.org/10.1186/s12977-020-00520-6 
    ​Details  DOI 
  • 2020 | Journal Article | 
    ​ ​Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software​
    Khalak, Y.; Tresadern, G.; de Groot, B. L.   & Gapsys, V. ​ (2020) 
    Journal of Computer-Aided Molecular Design, 35(1) pp. 49​-61​.​ DOI: https://doi.org/10.1007/s10822-020-00359-1 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset​
    Elisée, E.; Gapsys, V. ; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L.   & Iorga, B. I.​ (2019) 
    Journal of Computer-Aided Molecular Design, 33(12) pp. 1031​-1043​.​ DOI: https://doi.org/10.1007/s10822-019-00232-w 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype-phenotype correlation​
    Coci, E. G.; Gapsys, V. ; Shur, N.; Shin‐Podskarbi, Y.; de Groot, B. L. ; Miller, K. & Vockley, J. et al.​ (2019) 
    Human Mutation, 40(6) pp. 816​-827​.​ DOI: https://doi.org/10.1002/humu.23742 
    ​Details  DOI 
  • 2019 | Journal Article
    ​ ​Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches​
    Aldeghi, M.; Gapsys, V.   & de Groot, B. L. ​ (2019) 
    ACS Central Science, 5(8) pp. 1468​-1474​.​ DOI: https://doi.org/10.1021/acscentsci.9b00590 
    ​Details  DOI 
  • 2019 | Journal Article | 
    ​ ​Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'​
    Gapsys, V.   & de Groot, B. L. ​ (2019) 
    eLife, 8.​ DOI: https://doi.org/10.7554/eLife.44718 
    ​Details  DOI 
  • 2018 | Journal Article
    ​ ​Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets​
    Sabo, T. M. ; Gapsys, V. ; Walter, K. F. A.; Fenwick, R. B.; Becker, S. ; Salvatella, X. & de Groot, B. L.  et al.​ (2018) 
    Methods, 138-139 pp. 85​-92​.​ DOI: https://doi.org/10.1016/j.ymeth.2018.04.007 
    ​Details  DOI 
  • 2018 | Journal Article
    ​ ​Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation​
    Aldeghi, M.; Gapsys, V.   & de Groot, B. L. ​ (2018) 
    ACS Central Science, 4(12) pp. 1708​-1718​.​ DOI: https://doi.org/10.1021/acscentsci.8b00717 
    ​Details  DOI 
  • 2018 | Journal Article
    ​ ​A Unified Framework for Alchemical Mutations in Proteins, DNA and Ligands​
    Gapsys, V.   & de Groot, B. L. ​ (2018) 
    Biophysical Journal, 114(3) pp. 674a​.​ DOI: https://doi.org/10.1016/j.bpj.2017.11.3634 
    ​Details  DOI 
  • 2018 | Journal Article
    ​ ​Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations​
    Bastys, T.; Gapsys, V. ; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.   & Kalinina, O. V.​ (2018) 
    Journal of Chemical Theory and Computation, 14(7) pp. 3397​-3408​.​ DOI: https://doi.org/10.1021/acs.jctc.7b01109 
    ​Details  DOI 
  • 2017 | Journal Article
    ​ ​pmx Webserver: A User Friendly Interface for Alchemistry​
    Gapsys, V.   & de Groot, B. L. ​ (2017) 
    Journal of Chemical Information and Modeling, 57(2) pp. 109​-114​.​ DOI: https://doi.org/10.1021/acs.jcim.6b00498 
    ​Details  DOI 
  • 2017 | Journal Article
    ​ ​Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes​
    Gapsys, V.   & de Groot, B. L. ​ (2017) 
    Journal of Chemical Theory and Computation, 13(12) pp. 6275​-6289​.​ DOI: https://doi.org/10.1021/acs.jctc.7b00849 
    ​Details  DOI 
  • 2017 | Journal Article
    ​ ​Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation​
    Matthes, D. ; Gapsys, V. ; Griesinger, C.   & de Groot, B. L. ​ (2017) 
    ASC Chemical Neuroscience, 8(12) pp. 2791​-2808​.​ DOI: https://doi.org/10.1021/acschemneuro.7b00325 
    ​Details  DOI  PMID  PMC 
  • 2016 | Journal Article
    ​ ​Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC​
    Ilgü, H.; Jeckelmann, J.-M.; Gapsys, V. ; Ucurum, Z.; de Groot, B. L.   & Fotiadis, D.​ (2016) 
    Proceedings of the National Academy of Sciences of the United States of America, 113(37) pp. 10358​-10363​.​ DOI: https://doi.org/10.1073/pnas.1605442113 
    ​Details  DOI 
  • 2016 | Journal Article
    ​ ​Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan​
    Gapsys, V. ; Michielssens, S.; Seeliger, D. & de Groot, B. L. ​ (2016) 
    Angewandte Chemie. International Edition, 55(26) pp. 7364​-7368​.​ DOI: https://doi.org/10.1002/anie.201510054 
    ​Details  DOI 
  • 2016 | Journal Article
    ​ ​Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment​
    Rauscher, S.; Gapsys, V. ; Zhou, M.; Van, Q. ; Gajda, M.; Zweckstetter, M.   & Enderlein, J.  et al.​ (2016) 
    Biophysical Journal, 110(3) pp. 358a​.​ DOI: https://doi.org/10.1016/j.bpj.2015.11.1932 
    ​Details  DOI 
  • 2016 | Journal Article
    ​ ​Global and Local Conformational Heterogeniety Governs the Pre-Nucleation Phase in Amyloidogenic Self-Assembly​
    Matthes, D. ; Gapsys, V. ; Brennecke, J. T. & de Groot, B. L. ​ (2016) 
    Biophysical Journal, 110(3) pp. 402a​.​ DOI: https://doi.org/10.1016/j.bpj.2015.11.2170 
    ​Details  DOI 
  • 2016 | Journal Article
    ​ ​Insights from the First Principles Based Large Scale Protein Thermostability Calculations​
    Gapsys, V. ; Michielssens, S.; Seeliger, D. & de Groot, B. L. ​ (2016) 
    Biophysical Journal, 110(3) pp. 368a​.​ DOI: https://doi.org/10.1016/j.bpj.2015.11.1985 
    ​Details  DOI 
  • 2016 | Journal Article | 
    ​ ​An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase​
    Matthes, D. ; Gapsys, V. ; Brennecke, J. T. & de Groot, B. L. ​ (2016) 
    Scientific Reports, 6(1).​ DOI: https://doi.org/10.1038/srep33156 
    ​Details  DOI 
  • 2015 | Journal Article
    ​ ​Structural Ensembles of Intrinsically Disordered Proteins using Molecular Dynamics Simulation​
    Rauscher, S.; Gapsys, V. ; de Groot, B. L.   & Grubmüller, H. ​ (2015) 
    Biophysical Journal, 108(2) pp. 14a​.​ DOI: https://doi.org/10.1016/j.bpj.2014.11.100 
    ​Details  DOI 
  • 2015 | Journal Article | Research Paper
    ​ ​Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment​
    Rauscher, S.; Gapsys, V. ; Gajda, M. J.; Zweckstetter, M. ; Groot, B. L. de   & Grubmüller, H. ​ (2015) 
    Journal of Chemical Theory and Computation, 11(11) pp. 5513​-5524​.​ DOI: https://doi.org/10.1021/acs.jctc.5b00736 
    ​Details  DOI  PMID  PMC  WoS 
  • 2015 | Journal Article
    ​ ​Improved validation of IDP ensembles by one-bond C alpha-H alpha scalar couplings​
    Gapsys, V. ; Narayanan, R. L.; Xiang, S.; de Groot, B. L.   & Zweckstetter, M. ​ (2015) 
    Journal of Biomolecular NMR, 63(3) pp. 299​-307​.​ DOI: https://doi.org/10.1007/s10858-015-9990-z 
    ​Details  DOI  PMID  PMC  WoS 
  • 2013 | Journal Article
    ​ ​Optimal Superpositioning of Flexible Molecule Ensembles​
    Gapsys, V.   & de Groot, B. L. ​ (2013) 
    Biophysical Journal, 104(1) pp. 196​-207​.​ DOI: https://doi.org/10.1016/j.bpj.2012.11.003 
    ​Details  DOI 
  • 2013 | Journal Article | 
    ​ ​Computational analysis of local membrane properties​
    Gapsys, V. ; de Groot, B. L.   & Briones, R. ​ (2013) 
    Journal of Computer-Aided Molecular Design, 27(10) pp. 845​-858​.​ DOI: https://doi.org/10.1007/s10822-013-9684-0 
    ​Details  DOI 
  • 2013 | Journal Article | Research Paper
    ​ ​Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins​
    Xiang, S.; Gapsys, V. ; Kim, H.-Y.; Bessonov, S.; Hsiao, H.-H.; Moehlmann, S. & Klaukien, V. et al.​ (2013) 
    Structure, 21(12) pp. 2162​-2174​.​ DOI: https://doi.org/10.1016/j.str.2013.09.014 
    ​Details  DOI  PMID  PMC  WoS 
  • 2012 | Journal Article
    ​ ​Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations​
    Matthes, D. ; Gapsys, V.   & de Groot, B. L. ​ (2012) 
    Journal of Molecular Biology, 421(2-3) pp. 390​-416​.​ DOI: https://doi.org/10.1016/j.jmb.2012.02.004 
    ​Details  DOI 
  • 2012 | Journal Article
    ​ ​Non-Equilibrium Free Energy Calculations for Ligand Optimization​
    Gapsys, V. ; Seeliger, D. & de Groot, B. L. ​ (2012) 
    Biophysical Journal, 102(3) pp. 40a​.​ DOI: https://doi.org/10.1016/j.bpj.2011.11.249 
    ​Details  DOI 
  • 2012 | Journal Article
    ​ ​New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations​
    Gapsys, V. ; Seeliger, D. & de Groot, B. L. ​ (2012) 
    Journal of Chemical Theory and Computation, 8(7) pp. 2373​-2382​.​ DOI: https://doi.org/10.1021/ct300220p 
    ​Details  DOI 
  • 2011 | Journal Article
    ​ ​Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization​
    Matthes, D. ; Gapsys, V. ; Daebel, V. & de Groot, B. L. ​ (2011) 
    PLoS One, 6(5) pp. e19129​.​ DOI: https://doi.org/10.1371/journal.pone.0019129 
    ​Details  DOI 

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