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Authors whose works are in public domain in at least one jurisdiction

List of works by Bert L de Groot

1-50 of 169 results

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