Publications of Bert L. de Groot
All genres
Journal Article (198)
Journal Article
Resolving coupled pH titrations using alchemical free energy calculations. Journal of Computational Chemistry (2024)
Journal Article
121 (7), e2319682121 (2024)
Molecular basis for human aquaporin inhibition. PNAS
Journal Article
20 (2), pp. 914 - 925 (2024)
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of Chemical Theory and Computation
Journal Article
19 (21), pp. 7833 - 7845 (2023)
Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation
Journal Article
155 (8), e202213166 (2023)
Interactions between selectivity filter and pore helix control filter gating in the MthK channel. Journal of General Physiology
Journal Article
19 (9), pp. 2574 - 2589 (2023)
Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation
Journal Article
6, 82 (2023)
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications Chemistry
Journal Article
14 (1), 2178 (2023)
Central cavity dehydration as a gating mechanism of potassium channels. Nature Communications
Journal Article
299 (4), 103034 (2023)
Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. The Journal of Biological Chemistry
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
Journal Article
13 (1), 6810 (2022)
The 3D structure of lipidic fibrils of α-synuclein. Nature Communications
Journal Article
18 (10), pp. 6259 - 6270 (2022)
Chemical Space Exploration with Active Learning and Alchemical Free Energies. Journal of Chemical Theory and Computation
Journal Article
13, pp. 5385 - 5394 (2022)
The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature Communications
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
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
Journal Article
144 (9), pp. 4147 - 4157 (2022)
Direct detection of bound ammonium ions in the selectivity filter of ion channels by solid-state NMR. Journal of the American Chemical Society
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
Journal Article
13, 3792 (2022)
A litmus test for classifying recognition mechanisms of transiently binding proteins. Nature Communications
Journal Article
12, pp. 13958 - 13971 (2021)
Alchemical absolute protein-ligand binding free energies for drug design. Chemical Science
Journal Article
433 (17), 167002 (2021)
The persistent question of potassium channel permeation mechanisms. Journal of Molecular Biology