PubRank

Bert L de Groot

Author PubWeight™ 86.90‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 2008 8.04
2 Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des 2010 2.67
3 Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J 2006 2.19
4 Predicting free energy changes using structural ensembles. Nat Methods 2009 1.93
5 Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data. Biophys J 2010 1.75
6 Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci U S A 2008 1.67
7 Structure and function of water channels. Curr Opin Struct Biol 2002 1.55
8 Quaternary ammonium compounds as water channel blockers. Specificity, potency, and site of action. J Biol Chem 2006 1.46
9 Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations. Biophys J 2008 1.43
10 Crystal structure of a yeast aquaporin at 1.15 angstrom reveals a novel gating mechanism. PLoS Biol 2009 1.41
11 Protein thermostability calculations using alchemical free energy simulations. Biophys J 2010 1.33
12 Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. J Biomol NMR 2008 1.33
13 Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail. Biophys J 2011 1.30
14 Does CO2 permeate through aquaporin-1? Biophys J 2006 1.28
15 Detection of functional modes in protein dynamics. PLoS Comput Biol 2009 1.27
16 Geometry-based sampling of conformational transitions in proteins. Structure 2007 1.26
17 Speeding up parallel GROMACS on high-latency networks. J Comput Chem 2007 1.23
18 Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur Biophys J 2007 1.14
19 Functional dynamics in the voltage-dependent anion channel. Proc Natl Acad Sci U S A 2010 1.13
20 Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. J Biol Chem 2002 1.13
21 Normal modes and essential dynamics. Methods Mol Biol 2008 1.12
22 Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. J Mol Biol 2008 1.09
23 Short-range order and collective dynamics of DMPC bilayers: a comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments. Biophys J 2007 1.07
24 Kinetics of conformational sampling in ubiquitin. Angew Chem Int Ed Engl 2011 1.07
25 Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain. Mol Biol Cell 2005 1.06
26 Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes. Biophys J 2009 1.06
27 Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLoS Comput Biol 2012 1.04
28 Aquaporin-9 protein is the primary route of hepatocyte glycerol uptake for glycerol gluconeogenesis in mice. J Biol Chem 2011 1.04
29 β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure 2012 1.04
30 The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study. Structure 2008 1.03
31 Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handb Exp Pharmacol 2009 1.02
32 Voltage-regulated water flux through aquaporin channels in silico. Biophys J 2010 1.01
33 Conformational transitions upon ligand binding: holo-structure prediction from apo conformations. PLoS Comput Biol 2010 1.01
34 Determinants of water permeability through nanoscopic hydrophilic channels. Biophys J 2009 1.01
35 Molecular driving forces defining lipid positions around aquaporin-0. Proc Natl Acad Sci U S A 2012 0.99
36 Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. J Am Chem Soc 2010 0.97
37 Toward a consensus model of the HERG potassium channel. ChemMedChem 2010 0.95
38 Mobility of a one-dimensional confined file of water molecules as a function of file length. Phys Rev Lett 2006 0.95
39 Computational analysis of local membrane properties. J Comput Aided Mol Des 2013 0.94
40 The 4.5 A structure of human AQP2. J Mol Biol 2005 0.94
41 Partial least-squares functional mode analysis: application to the membrane proteins AQP1, Aqy1, and CLC-ec1. Biophys J 2012 0.94
42 A designed conformational shift to control protein binding specificity. Angew Chem Int Ed Engl 2014 0.93
43 The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure 2008 0.92
44 Discovery of novel human aquaporin-1 blockers. ACS Chem Biol 2012 0.92
45 Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Angew Chem Int Ed Engl 2005 0.91
46 Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc Natl Acad Sci U S A 2013 0.91
47 Population shuffling of protein conformations. Angew Chem Int Ed Engl 2014 0.91
48 Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length. Biophys J 2007 0.90
49 Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem Soc Trans 2008 0.90
50 Is TEA an inhibitor for human Aquaporin-1? Pflugers Arch 2008 0.90
51 Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. J Mol Biol 2012 0.88
52 Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. Phys Chem Chem Phys 2010 0.88
53 Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation. PLoS Comput Biol 2010 0.86
54 The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Mol Membr Biol 2013 0.85
55 Towards computational specificity screening of DNA-binding proteins. Nucleic Acids Res 2011 0.85
56 pmx: Automated protein structure and topology generation for alchemical perturbations. J Comput Chem 2014 0.84
57 Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophys J 2007 0.84
58 Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps. Proteins 2007 0.84
59 Ligand-release pathways in the pheromone-binding protein of Bombyx mori. Structure 2006 0.83
60 Phosphorylation of rat aquaporin-4 at Ser(111) is not required for channel gating. Glia 2013 0.83
61 Computer simulations of structure-activity relationships for HERG channel blockers. Biochemistry 2011 0.82
62 Mapping the conformational dynamics and pathways of spontaneous steric zipper Peptide oligomerization. PLoS One 2011 0.82
63 Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J 2005 0.81
64 Probing the energy landscape of activation gating of the bacterial potassium channel KcsA. PLoS Comput Biol 2013 0.81
65 A molecular switch driving inactivation in the cardiac K+ channel HERG. PLoS One 2012 0.81
66 Alternate structural conformations of Streptococcus pneumoniae hyaluronan lyase: insights into enzyme flexibility and underlying molecular mechanism of action. J Mol Biol 2006 0.81
67 Binding of glutamate to the umami receptor. Biophys Chem 2010 0.80
68 Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys J 2012 0.80
69 Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins 2009 0.79
70 The thermodynamic influence of trapped water molecules on a protein-ligand interaction. Angew Chem Int Ed Engl 2009 0.79
71 Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophys J 2008 0.79
72 Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Comput Biol 2013 0.79
73 Spontaneous aggregation of the insulin-derived steric zipper peptide VEALYL results in different aggregation forms with common features. J Mol Biol 2014 0.79
74 Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp. ChemMedChem 2012 0.77
75 Optimal superpositioning of flexible molecule ensembles. Biophys J 2013 0.77
76 How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochemistry 2013 0.76
77 Calculation of binding free energies. Methods Mol Biol 2015 0.76
78 Comment on "Molecular selectivity in aquaporin channels studied by the 3D-RISM theory". J Phys Chem B 2011 0.75
79 Molecular dynamics in principal component space. J Phys Chem B 2012 0.75
80 Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. J Chem Theory Comput 2017 0.75