Vytautas Gapsys

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  • 2022 Journal Article | 
    ​ ​Chakrabarti, Kalyan S., et al. "A litmus test for classifying recognition mechanisms of transiently binding proteins​." ​Nature Communications, vol. 13, no. 1, ​2022, , ​doi: 10.1038/s41467-022-31374-5. 
    Details  DOI 
  • 2022 Journal Article | 
    ​ ​Khalak, Yuriy, et al. "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, Miłosz, 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, Vytautas, et al. "Large scale relative protein ligand binding affinities using non-equilibrium alchemy​." ​Chemical Science, vol. 11, no. 4, ​2020, pp. 1140​-1152​, ​doi: 10.1039/C9SC03754C. 
    Details  DOI 
  • 2020 Journal Article
    ​ ​Rizzi, Andrea, et al. "The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations​." ​Journal of Computer-Aided Molecular Design, vol. 34, no. 5, ​2020, pp. 601​-633​, ​doi: 10.1007/s10822-020-00290-5. 
    Details  DOI 
  • 2020 Journal Article
    ​ ​Gapsys, Vytautas, et al. "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, vol. 124, no. 6, ​2020, pp. 1115​-1123​, ​doi: 10.1021/acs.jpcb.8b04187. 
    Details  DOI 
  • 2020 Journal Article | 
    ​ ​Khalak, Yuriy, et al. "Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software​." ​Journal of Computer-Aided Molecular Design, vol. 35, no. 1, ​2020, pp. 49​-61​, ​doi: 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, vol. 9, ​2020, , ​doi: 10.7554/eLife.57589. 
    Details  DOI 
  • 2020 Journal Article | 
    ​ ​Bastys, Tomas, et al. "Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors​." ​Retrovirology, vol. 17, no. 1, ​2020, , ​doi: 10.1186/s12977-020-00520-6. 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Coci, Emanuele G., 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, vol. 40, no. 6, ​2019, pp. 816​-827​, ​doi: 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, vol. 5, no. 8, ​2019, pp. 1468​-1474​, ​doi: 10.1021/acscentsci.9b00590. 
    Details  DOI 
  • 2019 Journal Article
    ​ ​Elisée, Eddy, 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, vol. 33, no. 12, ​2019, pp. 1031​-1043​, ​doi: 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, vol. 8, ​2019, , ​doi: 10.7554/eLife.44718. 
    Details  DOI 
  • 2018 Journal Article
    ​ ​Sabo, T. Michael, 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, vol. 138-139, ​2018, pp. 85​-92​, ​doi: 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, vol. 114, no. 3, ​2018, p. 674a​, ​doi: 10.1016/j.bpj.2017.11.3634. 
    Details  DOI 
  • 2018 Journal Article
    ​ ​Bastys, Tomas, et al. "Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations​." ​Journal of Chemical Theory and Computation, vol. 14, no. 7, ​2018, pp. 3397​-3408​, ​doi: 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, vol. 4, no. 12, ​2018, pp. 1708​-1718​, ​doi: 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, vol. 13, no. 12, ​2017, pp. 6275​-6289​, ​doi: 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, vol. 57, no. 2, ​2017, pp. 109​-114​, ​doi: 10.1021/acs.jcim.6b00498. 
    Details  DOI 
  • 2017 Journal Article
    ​ ​Matthes, Dirk, et al. "Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation​." ​ASC Chemical Neuroscience, vol. 8, no. 12, ​2017, pp. 2791​-2808​, ​doi: 10.1021/acschemneuro.7b00325. 
    Details  DOI  PMID  PMC 
  • 2016 Journal Article
    ​ ​Rauscher, Sarah, et al. "Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment​." ​Biophysical Journal, vol. 110, no. 3, ​2016, p. 358a​, ​doi: 10.1016/j.bpj.2015.11.1932. 
    Details  DOI 
  • 2016 Journal Article | 
    ​ ​Matthes, Dirk, et al. "An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase​." ​Scientific Reports, vol. 6, no. 1, ​2016, , ​doi: 10.1038/srep33156. 
    Details  DOI 
  • 2016 Journal Article
    ​ ​Gapsys, Vytautas, et al. "Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan​." ​Angewandte Chemie. International Edition, vol. 55, no. 26, ​2016, pp. 7364​-7368​, ​doi: 10.1002/anie.201510054. 
    Details  DOI 
  • 2016 Journal Article
    ​ ​Matthes, Dirk, et al. "Global and Local Conformational Heterogeniety Governs the Pre-Nucleation Phase in Amyloidogenic Self-Assembly​." ​Biophysical Journal, vol. 110, no. 3, ​2016, p. 402a​, ​doi: 10.1016/j.bpj.2015.11.2170. 
    Details  DOI 
  • 2016 Journal Article
    ​ ​Gapsys, Vytautas, et al. "Insights from the First Principles Based Large Scale Protein Thermostability Calculations​." ​Biophysical Journal, vol. 110, no. 3, ​2016, p. 368a​, ​doi: 10.1016/j.bpj.2015.11.1985. 
    Details  DOI 
  • 2016 Journal Article
    ​ ​Ilgü, Hüseyin, et al. "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, vol. 113, no. 37, ​2016, pp. 10358​-10363​, ​doi: 10.1073/pnas.1605442113. 
    Details  DOI 
  • 2015 Journal Article
    ​ ​Rauscher, Sarah, et al. "Structural Ensembles of Intrinsically Disordered Proteins using Molecular Dynamics Simulation​." ​Biophysical Journal, vol. 108, no. 2, ​2015, p. 14a​, ​doi: 10.1016/j.bpj.2014.11.100. 
    Details  DOI 
  • 2015 Journal Article | Research Paper
    ​ ​Rauscher, Sarah, et al. "Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment​." ​Journal of Chemical Theory and Computation, vol. 11, no. 11, ​2015, pp. 5513​-5524​, ​doi: 10.1021/acs.jctc.5b00736. 
    Details  DOI  PMID  PMC  WoS 
  • 2015 Journal Article
    ​ ​Gapsys, Vytautas, et al. "Improved validation of IDP ensembles by one-bond C alpha-H alpha scalar couplings​." ​Journal of Biomolecular NMR, vol. 63, no. 3, ​2015, pp. 299​-307​, ​doi: 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, vol. 104, no. 1, ​2013, pp. 196​-207​, ​doi: 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, vol. 27, no. 10, ​2013, pp. 845​-858​, ​doi: 10.1007/s10822-013-9684-0. 
    Details  DOI 
  • 2013 Journal Article | Research Paper
    ​ ​Xiang, Shengqi, et al. "Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins​." ​Structure, vol. 21, no. 12, ​2013, pp. 2162​-2174​, ​doi: 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, vol. 421, no. 2-3, ​2012, pp. 390​-416​, ​doi: 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, vol. 102, no. 3, ​2012, p. 40a​, ​doi: 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, vol. 8, no. 7, ​2012, pp. 2373​-2382​, ​doi: 10.1021/ct300220p. 
    Details  DOI 
  • 2011 Journal Article
    ​ ​Matthes, Dirk, et al. "Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization​." ​PLoS One, vol. 6, no. 5, ​2011, p. e19129​, ​doi: 10.1371/journal.pone.0019129. 
    Details  DOI 

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