Vytautas Gapsys

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