Publications by authors named "Bert L de Groot"

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Atomistic Mechanism of Calcium-Mediated Inward Rectification of the MthK Potassium Channel by Solid-State NMR and MD Simulations.
Carl Öster, Reinier de Vries, Juan Li, Denis Qoraj, Sascha Lange, Bert L de Groot

J Am Chem Soc· December 2025

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Evaluation of the ABCG2 Charge Model in Protein-Ligand Binding Free-Energy Calculations.
Sudarshan Behera, Vytautas Gapsys, Bert L de Groot

J Chem Inf Model· November 2025

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Anle138b binds predominantly to the central cavity in lipidic Aβ₄₀ fibrils and modulates fibril formation.
Mookyoung Han, Benedikt Frieg, Dirk Matthes, Andrei Leonov, Sergey Ryazanov, Bert L de Groot

Nat Commun· October 2025

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From Selective Permeation to Physiology in Potassium Channels.
Sun-Joo Lee, Johanna Schillings, Reinier de Vries, Marcos Matamoros, Bert L de Groot

Function (Oxf)· October 2025

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Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.
Sudarshan Behera, David F Hahn, Carter J Wilson, Simone Marsili, Gary Tresadern, Bert L de Groot

J Chem Inf Model· July 2025

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Identification of allosteric sites and ligand-induced modulation in the dopamine receptor through large-scale alchemical mutation scan.
Lisa Schmidt, Bert L de Groot

Chem Sci· May 2025

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Effective polarization in potassium channel simulations: Ion conductance, occupancy, voltage response, and selectivity.
Chenggong Hui, Reinier de Vries, Wojciech Kopec, Bert L de Groot

Proc Natl Acad Sci U S A· May 2025

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Improving p Predictions with Reparameterized Force Fields and Free Energy Calculations.
Carter J Wilson, Vytautas Gapsys, Bert L de Groot

J Chem Theory Comput· April 2025

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The need to implement FAIR principles in biomolecular simulations.
Rommie E Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Bert L de Groot

Nat Methods· April 2025

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Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding.
Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M Rangwala, Bert L de Groot

J Phys Chem B· March 2025

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Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding.
Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M Rangwala, Bert L de Groot

bioRxiv· March 2025

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NOMPC ion channel hinge forms a gating spring that initiates mechanosensation.
Philip Hehlert, Thomas Effertz, Ruo-Xu Gu, Björn Nadrowski, Bart R H Geurten, Bert L de Groot

Nat Neurosci· February 2025

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Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster.
Carsten Kutzner, Vedran Miletić, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L de Groot

J Comput Chem· February 2025

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Lipidic folding pathway of α-Synuclein via a toxic oligomer.
Vrinda Sant, Dirk Matthes, Hisham Mazal, Leif Antonschmidt, Franz Wieser, Bert L de Groot

Nat Commun· January 2025

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Biomolecular simulations at the exascale: From drug design to organelles and beyond.
Vytautas Gapsys, Wojciech Kopec, Dirk Matthes, Bert L de Groot

Curr Opin Struct Biol· October 2024

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Effect of two activators on the gating of a K channel.
Edward Mendez-Otalvaro, Wojciech Kopec, Bert L de Groot

Biophys J· October 2024

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Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts.
Po-Lin Chiu, Juan D Orjuela, Bert L de Groot, Camilo Aponte Santamaría, Thomas Walz

Elife· September 2024

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Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.
David F Hahn, Vytautas Gapsys, Bert L de Groot, David L Mobley, Gary Tresadern

J Chem Inf Model· July 2024

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Selectivity filter mutations shift ion permeation mechanism in potassium channels.
Andrei Mironenko, Bert L de Groot, Wojciech Kopec

PNAS Nexus· July 2024

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Resolving coupled pH titrations using alchemical free energy calculations.
Carter J Wilson, Bert L de Groot, Vytautas Gapsys

J Comput Chem· June 2024

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Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts.
Po-Lin Chiu, Juan D Orjuela, Bert L de Groot, Camilo Aponte-Santamaría, Thomas Walz

bioRxiv· May 2024

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Molecular basis for human aquaporin inhibition.
Peng Huang, Hannah Åbacka, Carter J Wilson, Malene Lykke Wind, Michael Rűtzler, Bert L de Groot

Proc Natl Acad Sci U S A· February 2024

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Guidelines for Free-Energy Calculations Involving Charge Changes.
Drazen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L de Groot, Vytautas Gapsys

J Chem Theory Comput· January 2024

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Accurately Predicting Protein p Values Using Nonequilibrium Alchemy.
Carter J Wilson, Mikko Karttunen, Bert L de Groot, Vytautas Gapsys

J Chem Theory Comput· November 2023

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Interactions between selectivity filter and pore helix control filter gating in the MthK channel.
Wojciech Kopec, Andrew S Thomson, Bert L de Groot, Brad S Rothberg

J Gen Physiol· August 2023

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