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List of works by Bert L de Groot

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Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

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

scientific article published on 7 November 2016
Ligand docking and binding site analysis with PyMOL and Autodock/Vina

scientific article
Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles

scientific article published on 23 February 2006
Mechanism of selectivity in aquaporins and aquaglyceroporins.

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

scientific article published on 01 October 2003
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

scientific article published on October 22, 2015
Predicting free energy changes using structural ensembles

scientific article published on 01 January 2009
The dynamics and energetics of water permeation and proton exclusion in aquaporins

scientific article
Structure and function of water channels.

scientific article
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

scientific article
Crystal Structure of a Yeast Aquaporin at 1.15 Å Reveals a Novel Gating Mechanism

scientific article
Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations.

scientific article
Ion permeation in K⁺ channels occurs by direct Coulomb knock-on.

scientific article published in October 2014
Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail

scientific article
Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments

scientific article published on 28 June 2007
Does CO2 permeate through aquaporin-1?

scientific article published on 12 May 2006
Detection of functional modes in protein dynamics

scientific article (publication date: August 2009)
Functional dynamics in the voltage-dependent anion channel

scientific article
Mechanisms of anion conduction by coupled glutamate transporters

scientific article published on January 2015
Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action

scientific article published on 21 March 2006
β-Barrel mobility underlies closure of the voltage-dependent anion channel

scientific article
Geometry-based sampling of conformational transitions in proteins.

scientific article published in November 2007
Protein thermostability calculations using alchemical free energy simulations

scientific article
Speeding up parallel GROMACS on high-latency networks

scientific article
Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate

scientific article
A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K(+) Channels.

scientific article published on February 2016
Crystal structure and functional mechanism of a human antimicrobial membrane channel

scientific article
Normal modes and essential dynamics

scientific article published in January 2008
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics

scientific article
Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins

scientific article published on October 31, 2013
Aquaporin-9 protein is the primary route of hepatocyte glycerol uptake for glycerol gluconeogenesis in mice

scientific article
Computational analysis of local membrane properties

scientific article published on October 23, 2013
Conformational transitions upon ligand binding: holo-structure prediction from apo conformations

scientific article
Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p

scientific article
Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain.

scientific article
Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations?

scientific article published on January 2009
Kinetics of Conformational Sampling in Ubiquitin

scientific article published on 05 October 2011
Toward a consensus model of the HERG potassium channel

scientific article published in March 2010
Crystal Structure of an Ammonia-Permeable Aquaporin

scientific article
Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study

scientific article published on June 2002
Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes.

scientific article
Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection

scientific article
Molecular driving forces defining lipid positions around aquaporin-0.

scientific article
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

scientific article published on August 4, 2015
Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes

scientific article published in July 2009
pmx: Automated protein structure and topology generation for alchemical perturbations

scientific article published on December 8, 2014
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

scientific article published on 2 January 2014
The 4.5Å Structure of Human AQP2

The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study

scientific article published on August 2008

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