Bert L. de Groot

Research interests

Publications

• Large scale relative protein ligand binding affinities using non-equilibrium alchemy

  Chemical Science · 2019 · https://doi.org/10.1039/c9sc03754c

• More bang for your buck: Improved use of GPU nodes for GROMACS 2018

  Journal of Computational Chemistry · 2019 · https://doi.org/10.1002/jcc.26011

• Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

  Nature Chemistry · 2018 · https://doi.org/10.1038/s41557-018-0105-9

• CHARMM36m: an improved force field for folded and intrinsically disordered proteins

  Nature Methods · 2016 · https://doi.org/10.1038/nmeth.4067

• Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

  Journal of Chemical Theory and Computation · 2015 · https://doi.org/10.1021/acs.jctc.5b00736

• Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

  Journal of Computational Chemistry · 2015 · https://doi.org/10.1002/jcc.24030

• pmx: Automated protein structure and topology generation for alchemical perturbations

  Journal of Computational Chemistry · 2014 · https://doi.org/10.1002/jcc.23804

• Ion permeation in K + channels occurs by direct Coulomb knock-on

  Science · 2014 · https://doi.org/10.1126/science.1254840

• Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

  Journal of Chemical Theory and Computation · 2013 · https://doi.org/10.1021/ct400626b

• Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail

  Biophysical Journal · 2011 · https://doi.org/10.1016/j.bpj.2011.06.010

• g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

  Journal of Chemical Theory and Computation · 2010 · https://doi.org/10.1021/ct100494z

• Ligand docking and binding site analysis with PyMOL and Autodock/Vina

  Journal of Computer-Aided Molecular Design · 2010 · https://doi.org/10.1007/s10822-010-9352-6

• Protein Thermostability Calculations Using Alchemical Free Energy Simulations

  Biophysical Journal · 2010 · https://doi.org/10.1016/j.bpj.2010.01.051

• Mechanism of selectivity in aquaporins and aquaglyceroporins

  Proceedings of the National Academy of Sciences · 2008 · https://doi.org/10.1073/pnas.0707662104

• Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations

  Biophysical Journal · 2008 · https://doi.org/10.1529/biophysj.108.129437

• Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

  Science · 2008 · https://doi.org/10.1126/science.1157092

• Predicting free energy changes using structural ensembles

  Nature Methods · 2008 · https://doi.org/10.1038/nmeth0109-3

• Sequential N‐ to C‐terminal SNARE complex assembly drives priming and fusion of secretory vesicles

  The EMBO Journal · 2006 · https://doi.org/10.1038/sj.emboj.7601003

• Molecular Anatomy of a Trafficking Organelle

  Cell · 2006 · https://doi.org/10.1016/j.cell.2006.10.030

• The dynamics and energetics of water permeation and proton exclusion in aquaporins

  Current Opinion in Structural Biology · 2005 · https://doi.org/10.1016/j.sbi.2005.02.003

• The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

  Journal of Molecular Biology · 2003 · https://doi.org/10.1016/j.jmb.2003.08.003

• Structure and Function of Water Channels

  Current Opinion in Structural Biology · 2002 · https://doi.org/10.1016/s0959-440x(02)00355-x

• Water Permeation Across Biological Membranes: Mechanism and Dynamics of Aquaporin-1 and GlpF

  Science · 2001 · https://doi.org/10.1126/science.1066115

• Prediction of protein conformational freedom from distance constraints

  Proteins Structure Function and Bioinformatics · 1997 · https://doi.org/10.1002/(sici)1097-0134(199710)29:2<240::aid-prot11>3.0.co;2-o

• An Efficient Method for Sampling the Essential Subspace of Proteins

  Journal of Biomolecular Structure and Dynamics · 1996 · https://doi.org/10.1080/07391102.1996.10508874

Current projects

No projects listed.