Bert L. de Groot

29 papers Journal 28Unranked 1

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Evaluation of the ABCG2 Charge Model in Protein-Ligand Binding Free-Energy Calculations. J. Chem. Inf. Model. Sudarshan Behera, Vytautas Gapsys, Bert L. de Groot
2025	J	`jnl`	Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy. J. Chem. Inf. Model. Sudarshan Behera, David F. Hahn, Carter J. Wilson, Simone Marsili, Gary Tresadern, Vytautas Gapsys, Bert L. de Groot
2025	J	`jnl`	Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. J. Comput. Chem. Carsten Kutzner, Vedran Miletic, Karen Palacio Rodríguez, Markus Rampp, Gerhard Hummer, Bert L. de Groot, Helmut Grubmüller
2024	J	`jnl`	Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J. Chem. Inf. Model. David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern
2024	J	`jnl`	Resolving coupled pH titrations using alchemical free energy calculations. J. Comput. Chem. Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys
2022	J	`jnl`	GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design. J. Chem. Inf. Model. Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys
2022	J	`jnl`	GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. CoRR Carsten Kutzner, Christian Kniep, Austin Cherian, Ludvig Nordstrom, Helmut Grubmüller, Bert L. de Groot, Vytautas Gapsys
2022	J	`jnl`	Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design. J. Chem. Inf. Model. Vytautas Gapsys, David F. Hahn, Gary Tresadern, David L. Mobley, Markus Rampp, Bert L. de Groot
2021	J	`jnl`	Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. J. Comput. Aided Mol. Des. Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys
2020	J	`jnl`	The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 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
2019	J	`jnl`	More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018. CoRR Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2019	J	`jnl`	More bang for your buck: Improved use of GPU nodes for GROMACS 2018. J. Comput. Chem. Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2019	J	`jnl`	Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. J. Comput. Aided Mol. Des. Eddy Elisée, Vytautas Gapsys, Nawel Mele, Ludovic Chaput, Edithe Selwa, Bert L. de Groot, Bogdan I. Iorga
2017	J	`jnl`	pmx Webserver: A User Friendly Interface for Alchemistry. J. Chem. Inf. Model. Vytautas Gapsys, Bert L. de Groot
2015	J	`jnl`	Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. CoRR Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2015	J	`jnl`	Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comput. Chem. Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
2015	J	`jnl`	pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comput. Chem. Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot
2013	J	`jnl`	Collective Dynamics Underlying Allosteric Transitions in Hemoglobin. PLoS Comput. Biol. Martin D. Vesper, Bert L. de Groot
2013	J	`jnl`	Computational analysis of local membrane properties. J. Comput. Aided Mol. Des. Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones
2013	J	`jnl`	Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA. PLoS Comput. Biol. Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger
2012	J	`jnl`	Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection. PLoS Comput. Biol. Jan H. Peters, Bert L. de Groot
2010	J	`jnl`	Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations. PLoS Comput. Biol. Daniel Seeliger, Bert L. de Groot
2010	J	`jnl`	Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. Daniel Seeliger, Bert L. de Groot
2010	J	`jnl`	Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation. PLoS Comput. Biol. Jochen S. Hub, Marcus B. Kubitzki, Bert L. de Groot
2009	J	`jnl`	Detection of Functional Modes in Protein Dynamics. PLoS Comput. Biol. Jochen S. Hub, Bert L. de Groot
2009	J	`jnl`	tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules. J. Comput. Chem. Daniel Seeliger, Bert L. de Groot
2007	J	`jnl`	Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
2006	—	`conf`	Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
1997	J	`jnl`	A comparison of techniques for calculating protein essential dynamics. J. Comput. Chem. Daan M. F. van Aalten, Bert L. de Groot, John B. C. Findlay, Herman J. C. Berendsen, Andrea Amadei