Bert L de Groot (B L de Groot)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 57

Top Topics

Molecular Dynamics Simulations

Binding Protein

Drug Administration

Top Venues

Journal of chemical theory and computation

Communications chemistry

Journal of chemical information and modeling

Proceedings of the National Academy of Sciences of the United States of America

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)
Peng Huang, Hannah Åbacka, Carter J Wilson, Malene Lykke Wind, Michael Rűtzler, Anna Hagström-Andersson, Pontus Emanuel Gourdon, Bert L de Groot, Raminta Venskutonytė, Karin Lindkvist-Petersson
Molecular basis for human aquaporin inhibition. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (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)
Po-Lin Chiu, Juan D Orjuela, Bert L de Groot, Camilo Aponte-Santamaría, Thomas Walz
Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 12 (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)
Andrei Mironenko, Bert L de Groot, Wojciech Kopec
Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS nexus 3 (7) (2024)
Peng Huang, Hannah Åbacka, Carter J Wilson, Malene Lykke Wind, Michael Rűtzler, Anna Hagström-Andersson, Pontus Emanuel Gourdon, Bert L de Groot, Raminta Venskutonytė, Karin Lindkvist-Petersson
Molecular basis for human aquaporin inhibition. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (2024)
Andrei Mironenko, Bert L de Groot, Wojciech Kopec
Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS nexus 3 (7) (2024)
Po-Lin Chiu, Juan D Orjuela, Bert L de Groot, Camilo Aponte-Santamaría, Thomas Walz
Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 12 (2024)
Peng Huang, Hannah Åbacka, Carter J Wilson, Malene Lykke Wind, Michael Rűtzler, Anna Hagström-Andersson, Pontus Emanuel Gourdon, Bert L de Groot, Raminta Venskutonytė, Karin Lindkvist-Petersson
Molecular basis for human aquaporin inhibition. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (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 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)
Peng Huang, Hannah Åbacka, Carter J Wilson, Malene Lykke Wind, Michael Rűtzler, Anna Hagström-Andersson, Pontus Emanuel Gourdon, Bert L de Groot, Raminta Venskutonytė, Karin Lindkvist-Petersson
Molecular basis for human aquaporin inhibition. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (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)
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)
Chun Kei Lam, Bert L de Groot
Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. 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)
Wojciech Kopec, Andrew S Thomson, Bert L de Groot, Brad S Rothberg
Interactions between selectivity filter and pore helix control filter gating in the MthK channel. The Journal of general physiology 155 (8) (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)
Ruo-Xu Gu, Bert L de Groot
Central cavity dehydration as a gating mechanism of potassium channels. Nature communications 14 (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)
Carl Öster, Kumar Tekwani Movellan, Benjamin Goold, Kitty Hendriks, Sascha Lange, Stefan Becker, Bert L de Groot, Wojciech Kopec, Loren B Andreas, Sascha Lange
Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. Journal of the American Chemical Society 144 (9) (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)
Leif Antonschmidt, Dirk Matthes, Riza Dervişoğlu, Benedikt Frieg, Christian Dienemann, Andrei Leonov, Evgeny Nimerovsky, Vrinda Sant, Sergey Ryazanov, Armin Giese, Gunnar F Schröder, Stefan Becker, Bert L de Groot, Christian Griesinger, Loren B Andreas
The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature communications 13 (1) (2022)
Benedikt Frieg, Leif Antonschmidt, Christian Dienemann, James A Geraets, Eszter E Najbauer, Dirk Matthes, Bert L de Groot, Loren B Andreas, Stefan Becker, Christian Griesinger, Gunnar F Schröder
The 3D structure of lipidic fibrils of α-synuclein. Nature communications 13 (1) (2022)
Yixiao Zhang, Csaba Daday, Ruo-Xu Gu, Charles D Cox, Boris Martinac, Bert L de Groot, Thomas Walz
Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590 (7846) (2021)
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)
Floris P Buelens, Hadas Leonov, Bert L de Groot, Helmut Grubmüller
ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections. Journal of chemical theory and computation 17 (3) (2021)
Tobias Schubeis, Tanguy Le Marchand, Csaba Daday, Wojciech Kopec, Kumar Tekwani Movellan, Jan Stanek, Tom S Schwarzer, Kathrin Castiglione, Bert L de Groot, Guido Pintacuda, Loren B Andreas
A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America 117 (35) (2020)
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)
Csaba Daday, Bert L de Groot
Lipid-protein forces predict conformational changes in a mechanosensitive channel. European biophysics journal : EBJ 50 (2) (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)
Fabian Rabe von Pappenheim, Matteo Aldeghi, Brateen Shome, Tadhg Begley, Bert L de Groot, Kai Tittmann
Structural basis for antibiotic action of the B1 antivitamin 2'-methoxy-thiamine. Nature chemical biology 16 (11) (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)
Petra Rovó, Colin A Smith, Diego Gauto, Bert L de Groot, Paul Schanda, Rasmus Linser
Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques. Journal of the American Chemical Society 141 (2) (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)
Marcus Schewe, Han Sun, Ümit Mert, Alexandra Mackenzie, Ashley C W Pike, Friederike Schulz, Cristina Constantin, Kirsty S Vowinkel, Linus J Conrad, Aytuğ K Kiper, Wendy González, Marianne Musinszki, Marie Tegtmeier, David C Pryde, Hassane Belabed, Marc Nazare, Bert L de Groot, Niels Decher, Bernd Fakler, Elisabeth P Carpenter, Stephen J Tucker, Thomas Baukrowitz
A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science (New York, N.Y.) 363 (6429) (2019)
Carl Öster, Kitty Hendriks, Wojciech Kopec, Veniamin Chevelkov, Chaowei Shi, Dagmar Michl, Sascha Lange, Han Sun, Bert L de Groot, Sascha Lange
The conduction pathway of potassium channels is water free under physiological conditions. Science advances 5 (7) (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)
Helmut Lutz, Vance Jaeger, Tobias Weidner, Bert L de Groot
Interpretation of Interfacial Protein Spectra with Enhanced Molecular Simulation Ensembles. Journal of chemical theory and computation 15 (1) (2018)
Julian T Brennecke, Bert L de Groot
Quantifying Asymmetry of Multimeric Proteins. The journal of physical chemistry. A 122 (39) (2018)
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)
Wojciech Kopec, David A Köpfer, Owen N Vickery, Anna S Bondarenko, Thomas la Cour Jansen, Bert L de Groot, Ulrich Zachariae
Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature chemistry 10 (8) (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)
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)