Vytautas Gapsys

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

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