Bert L. de Groot

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 11

Top Topics

Belief Propagation

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

Publications

David F. Hahn, Vytautas Gapsys, Bert L. de Groot, David L. Mobley, Gary Tresadern
Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions. J. Chem. Inf. Model. 64 (13) (2024)
Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys
Resolving coupled pH titrations using alchemical free energy calculations. J. Comput. Chem. 45 (17) (2024)
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. CoRR (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. J. Chem. Inf. Model. 62 (7) (2022)
Vytautas Gapsys, David F. Hahn, Gary 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. J. Chem. Inf. Model. 62 (5) (2022)
Yuriy Khalak, Gary Tresadern, Bert L. de Groot, Vytautas Gapsys
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. J. Comput. Aided Mol. Des. 35 (1) (2021)
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. J. Comput. Aided Mol. Des. 34 (5) (2020)
Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
More bang for your buck: Improved use of GPU nodes for GROMACS 2018. J. Comput. Chem. 40 (27) (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. J. Comput. Aided Mol. Des. 33 (12) (2019)
Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018. CoRR (2019)
Vytautas Gapsys, Bert L. de Groot
pmx Webserver: A User Friendly Interface for Alchemistry. J. Chem. Inf. Model. 57 (2) (2017)
Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. CoRR (2015)
Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger, Bert L. de Groot
pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comput. Chem. 36 (5) (2015)
Carsten Kutzner, Szilárd Páll, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmüller
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comput. Chem. 36 (26) (2015)
Martin D. Vesper, Bert L. de Groot
Collective Dynamics Underlying Allosteric Transitions in Hemoglobin. PLoS Comput. Biol. 9 (9) (2013)
Vytautas Gapsys, Bert L. de Groot, Rodolfo Briones
Computational analysis of local membrane properties. J. Comput. Aided Mol. Des. 27 (10) (2013)
Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger
Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA. PLoS Comput. Biol. 9 (5) (2013)
Jan H. Peters, Bert L. de Groot
Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection. PLoS Comput. Biol. 8 (10) (2012)
Daniel Seeliger, Bert L. de Groot
Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations. PLoS Comput. Biol. 6 (1) (2010)
Daniel Seeliger, Bert L. de Groot
Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. 24 (5) (2010)
Jochen S. Hub, Marcus B. Kubitzki, Bert L. de Groot
Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation. PLoS Comput. Biol. 6 (5) (2010)
Daniel Seeliger, Bert L. de Groot
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules. J. Comput. Chem. 30 (7) (2009)
Jochen S. Hub, Bert L. de Groot
Detection of Functional Modes in Protein Dynamics. PLoS Comput. Biol. 5 (8) (2009)
Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. 28 (12) (2007)
Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI (2006)
Daan M. F. van Aalten, Bert L. de Groot, John B. C. Findlay, Herman J. C. Berendsen, Andrea Amadei
A comparison of techniques for calculating protein essential dynamics. J. Comput. Chem. 18 (2) (1997)