Vytautas Gapsys (V Gapsys)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 38

Top Topics

Molecular Dynamics Simulations

Binding Protein

Drug Administration

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

Communications chemistry

Journal of computer-aided molecular design

This page only lists publications with an associated author ORCID identifier.

Publications

Dražen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L de Groot, Vytautas Gapsys
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of chemical theory and computation (2024)
Dražen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L de Groot, Vytautas Gapsys
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of chemical theory and computation 20 (2) (2024)
David F Hahn, Vytautas Gapsys, Bert L de Groot, David L Mobley, Gary John Tresadern
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. Journal of chemical information and modeling 64 (13) (2024)
Carter J Wilson, Bert L de Groot, Vytautas Gapsys
Resolving coupled pH titrations using alchemical free energy calculations. Journal of computational chemistry (2024)
David F Hahn, Vytautas Gapsys, Bert L de Groot, David L Mobley, Gary John Tresadern
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. Journal of chemical information and modeling 64 (13) (2024)
Carter J Wilson, Bert L de Groot, Vytautas Gapsys
Resolving coupled pH titrations using alchemical free energy calculations. Journal of computational chemistry 45 (17) (2024)
Dražen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L de Groot, Vytautas Gapsys
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of chemical theory and computation 20 (2) (2024)
David F Hahn, Vytautas Gapsys, Bert L de Groot, David L Mobley, Gary John Tresadern
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. Journal of chemical information and modeling 64 (13) (2024)
Dražen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L de Groot, Vytautas Gapsys
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of chemical theory and computation 20 (2) (2024)
David F Hahn, Vytautas Gapsys, Bert L de Groot, David L Mobley, Gary John Tresadern
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. Journal of chemical information and modeling (2024)
Carter J Wilson, Jonathan F Lovell, Bert L de Groot, Vytautas Gapsys
Accurately Predicting Protein p K a Values Using Nonequilibrium Alchemy. Journal of chemical theory and computation (2023)
Simon Boothroyd, Pavan Kumar Behara, Owen C Madin, David F Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R Wagner, Joshua T Horton, David L Dotson, Matthew W Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J Cole, Michael K Gilson, John D Chodera, Christopher I Bayly, Michael R Shirts, David L Mobley
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of chemical theory and computation (2023)
J Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert L de Groot, Vytautas Gapsys
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications chemistry 6 (1) (2023)
J Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert L de Groot, Vytautas Gapsys
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications chemistry 6 (1) (2023)
J Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert L de Groot, Vytautas Gapsys
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications chemistry 6 (1) (2023)
J Harry Moore, Christian Margreitter, Jon Paul Janet, Ola Engkvist, Bert L de Groot, Vytautas Gapsys
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications chemistry 6 (1) (2023)
Kalyan S Chakrabarti, Simon Olsson, Supriya Pratihar, Karin Giller, Kerstin Overkamp, Ko On Lee, Vytautas Gapsys, Kyoung-Seok Ryu, Bert L de Groot, Frank Noé, Stefan Becker, Donghan Lee, Thomas R Weikl, Christian Griesinger
A litmus test for classifying recognition mechanisms of transiently binding proteins. Nature communications 13 (1) (2022)
Yuriy Khalak, Gary John Tresadern, David F Hahn, Bert L de Groot, Vytautas Gapsys
Chemical Space Exploration with Active Learning and Alchemical Free Energies. Journal of chemical theory and computation 18 (10) (2022)
Vytautas Gapsys, David F Hahn, Gary John Tresadern, David L Mobley, Markus Rampp, Bert L de Groot
Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. Journal of chemical information and modeling 62 (5) (2022)
Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L de Groot, Vytautas Gapsys
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. Journal of chemical information and modeling 62 (7) (2022)
Miłosz Wieczór, Vito Genna, Juan Aranda, Rosa M Badia, Josep Lluís Gelpí, Vytautas Gapsys, Bert L de Groot, Erik Lindahl, Martí Municoy, Adam Hospital, Modesto Orozco
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley interdisciplinary reviews. Computational molecular science (2022)
Y Khalak, Gary John Tresadern, Matteo Aldeghi, H M Baumann, D L Mobley, Bert L de Groot, Vytautas Gapsys
Alchemical absolute protein-ligand binding free energies for drug design. Chemical science 12 (41) (2021)
Hannah M Baumann, Vytautas Gapsys, Bert L de Groot, David L Mobley
Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations. The journal of physical chemistry. B 125 (17) (2021)
Martin Werner, Vytautas Gapsys, Bert L de Groot
One Plus One Makes Three: Triangular Coupling of Correlated Amino Acid Mutations. The journal of physical chemistry letters 12 (12) (2021)
Myeongkyu Kim, Jung-Hye Ha, Joonhyeok Choi, Bo-Ram Kim, Vytautas Gapsys, Ko On Lee, Jun-Goo Jee, Kalyan S Chakrabarti, Bert L de Groot, Christian Griesinger, Kyoung Seok Ryu, Donghan Lee
Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IXβ Reductase B as a Novel Thrombocytopenia Therapeutic Target. Journal of medicinal chemistry 65 (3) (2021)
Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David van der Spoel, Bert L de Groot
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications chemistry 4 (1) (2021)
Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David van der Spoel, Bert L de Groot
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications chemistry 4 (1) (2021)
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
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of computer-aided molecular design 34 (5) (2020)
Vytautas Gapsys, Bert L de Groot
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 9 (2020)
Wojciech Kopec, Agata Żak, Dorota Jamróz, Rina Nakahata, Shin-Ichi Yusa, Vytautas Gapsys, Mariusz Kępczyński
Polycation-Anionic Lipid Membrane Interactions. Langmuir : the ACS journal of surfaces and colloids 36 (42) (2020)
Yuriy Khalak, Gary John Tresadern, Bert L de Groot, Vytautas Gapsys
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of computer-aided molecular design 35 (1) (2020)
Vytautas Gapsys, Laura Perez Benito, Matteo Aldeghi, Daniel Seeliger, Herman W T van Vlijmen, Gary John Tresadern, Bert L de Groot
Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical science 11 (4) (2019)
Vytautas Gapsys, Bert L de Groot
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8 (2019)
Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L de Groot, 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 (12) (2019)
Tomas Bastys, Vytautas Gapsys, Nadezhda T Doncheva, Rolf Kaiser, Bert L de Groot, 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 (7) (2018)
Vytautas Gapsys, Bert L de Groot
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes. Journal of chemical theory and computation 13 (12) (2017)
Vytautas Gapsys, Bert L de Groot
pmx Webserver: A User Friendly Interface for Alchemistry. Journal of chemical information and modeling 57 (2) (2017)
Dirk Matthes, Vytautas Gapsys, Christian Griesinger, Bert L de Groot
Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation. ACS chemical neuroscience 8 (12) (2017)