Publications of Vytautas Gapsys
All genres
Journal Article (41)
1.
Journal Article
20 (2), pp. 914 - 925 (2024)
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of Chemical Theory and Computation 2.
Journal Article
19 (21), pp. 7833 - 7845 (2023)
Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation 3.
Journal Article
19 (11), pp. 3251 - 3275 (2023)
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation 4.
Journal Article
6, 82 (2023)
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications Chemistry 5.
Journal Article
13 (1), e1622 (2023)
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews: Computational Molecular Science 6.
Journal Article
18 (10), pp. 6259 - 6270 (2022)
Chemical Space Exploration with Active Learning and Alchemical Free Energies. Journal of Chemical Theory and Computation 7.
Journal Article
62 (7), pp. 1691 - 1711 (2022)
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. Journal of Chemical Information and Modeling 8.
Journal Article
62 (5), pp. 1172 - 1177 (2022)
Pre-exascale computing of protein-ligand binding free energies with open source software for drug design. Journal of Chemical Information and Modeling 9.
Journal Article
65 (3), pp. 2548 - 2557 (2022)
Repositioning food and drug administration-approved drugs for inhibiting Biliverdin IXβ reductase B as a novel thrombocytopenia therapeutic target. Journal of Medicinal Chemistry 10.
Journal Article
12, pp. 13958 - 13971 (2021)
Alchemical absolute protein-ligand binding free energies for drug design. Chemical Science 11.
Journal Article
4, 61 (2021)
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 12.
Journal Article
125 (17), pp. 4241 - 4261 (2021)
Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 13.
Journal Article
12 (12), pp. 3195 - 3201 (2021)
One plus one makes three: Triangular coupling of correlated amino acid mutations. Journal of Physical Chemistry Letters 14.
Journal Article
35 (1), pp. 49 - 61 (2021)
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design 15.
Journal Article
9, e57589 (2020)
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 16.
Journal Article
17, 13 (2020)
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 17.
Journal Article
34 (5), pp. 601 - 633 (2020)
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design 18.
Journal Article
124 (6), pp. 1115 - 1123 (2020)
Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes". The Journal of Physical Chemistry B 19.
Journal Article
11 (4), pp. 1140 - 1152 (2020)
Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science 20.
Journal Article
33, pp. 1031 - 1043 (2019)
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design