Vytautas Gapsys

13 papers Journal 13
YearRankTypeTitle / Venue / Authors
2025 J jnl
Evaluation of the ABCG2 Charge Model in Protein-Ligand Binding Free-Energy Calculations.
J. Chem. Inf. Model.
Sudarshan Behera, Vytautas Gapsys, Bert L. de Groot
2025 J jnl
Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.
J. Chem. Inf. Model.
Sudarshan Behera, David F. Hahn, Carter J. Wilson, Simone Marsili, Gary Tresadern, Vytautas Gapsys, Bert L. de Groot
2024 J jnl
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.
J. Chem. Inf. Model.
David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern
2024 J jnl
Resolving coupled pH titrations using alchemical free energy calculations.
J. Comput. Chem.
Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys
2022 J jnl
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design.
J. Chem. Inf. Model.
Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys
2022 J jnl
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design.
CoRR
Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys
2022 J jnl
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.
J. Chem. Inf. Model.
Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
2021 J jnl
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.
J. Comput. Aided Mol. Des.
Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys
2020 J jnl
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
J. Comput. Aided Mol. Des.
Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera
2019 J jnl
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.
J. Comput. Aided Mol. Des.
Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
2017 J jnl
pmx Webserver: A User Friendly Interface for Alchemistry.
J. Chem. Inf. Model.
Vytautas Gapsys, Bert L. de Groot
2015 J jnl
pmx: Automated protein structure and topology generation for alchemical perturbations.
J. Comput. Chem.
Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot
2013 J jnl
Computational analysis of local membrane properties.
J. Comput. Aided Mol. Des.
Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones