Wilfred F. Van Gunsteren

Wilfred F. Van Gunsteren's AcademicInfluence.com Rankings

Chemistry

#3438

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#4456

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chemistry Degrees

Wilfred F. Van Gunsteren

Physics

#5821

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#7698

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Biophysics

#223

World Rank

#234

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Chemistry
Physics

Wilfred F. Van Gunsteren's Degrees

PhD Chemistry University of Amsterdam

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Wilfred F. Van Gunsteren's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

A consistent empirical potential for water–protein interactions (1984) (691)
Biomolecular modeling: Goals, problems, perspectives. (2006) (456)
A protein structure from nuclear magnetic resonance data. lac repressor headpiece. (1985) (426)
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. (1995) (359)
Reversible peptide folding in solution by molecular dynamics simulation. (1998) (334)
Folding–unfolding thermodynamics of a β‐heptapeptide from equilibrium simulations (1999) (318)
Practical Aspects of Free-Energy Calculations: A Review. (2014) (316)
Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. (1994) (270)
Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. (1990) (242)
Molecular dynamics simulations. (2002) (226)
On developing coarse-grained models for biomolecular simulation: a review. (2012) (212)
A comparison of methods to compute the potential of mean force. (2007) (210)
Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. (1993) (199)
Protein structures from NMR. (1988) (187)
Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A: evidence from partition coefficients and molecular dynamics simulations. (1993) (179)
Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice. (2004) (178)
Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. (1982) (176)
Molecular simulation as an aid to experimentalists. (2008) (172)
GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. (2011) (171)
Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. (1983) (170)
Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding. (2011) (149)
Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature. (2001) (146)
Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation (2002) (146)
The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation. (2001) (139)
Time dependence of atomic fluctuations in proteins: analysis of local and collective motions in bovine pancreatic trypsin inhibitor. (1982) (139)
A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein. Secondary structure motion in a 150 picosecond trajectory. (1985) (127)
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state. (1992) (127)
An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. (1996) (126)
Estimating entropies from molecular dynamics simulations. (2004) (126)
The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State. (2001) (124)
A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations (2002) (122)
On the interpretation of biochemical data by molecular dynamics computer simulation. (1992) (120)
A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. (2011) (115)
Assessing equilibration and convergence in biomolecular simulations (2002) (114)
Enveloping distribution sampling: a method to calculate free energy differences from a single simulation. (2007) (112)
New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters. (2011) (109)
Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state. (1984) (108)
Comparing geometric and kinetic cluster algorithms for molecular simulation data. (2010) (108)
Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex. (2010) (108)
Unusual compactness of a polyproline type II structure. (2005) (107)
Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes. (1995) (105)
Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. (1990) (104)
On the Choice of Dihedral Angle Potential Energy Functions for n-Alkanes (2000) (104)
Recent advances in computational actinoid chemistry. (2012) (103)
Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. (2006) (102)
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. (2007) (99)
Free energies of ligand binding for structurally diverse compounds. (2005) (98)
A photoinducible beta-hairpin. (2005) (98)
On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. (2009) (97)
Configurational entropy elucidates the role of salt‐bridge networks in protein thermostability (2007) (95)
Conformational and dynamical properties of disaccharides in water: a molecular dynamics study. (2006) (93)
The effect of motional averaging on the calculation of NMR‐derived structural properties (1999) (90)
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study (1995) (89)
Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data. (1989) (88)
A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease. (1996) (86)
Validation of Molecular Simulation: An Overview of Issues. (2018) (85)
Conformational differences between alpha-cyclodextrin in aqueous solution and in crystalline form. A molecular dynamics study. (1988) (85)
Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups. (2009) (84)
Can the stability of protein mutants be predicted by free energy calculations? (1993) (83)
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation (2003) (82)
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations (2001) (82)
Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us? (2006) (81)
Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions. (2008) (81)
On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm. (2007) (79)
The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. (1995) (78)
Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. (2011) (77)
Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D. (2009) (77)
A structure refinement method based on molecular dynamics in four spatial dimensions. (1993) (76)
Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. (1998) (75)
Molecular mechanics in biology: from structure to function, taking account of solvation. (1994) (73)
Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: Application to the DNA binding domain of lac repressor from Escherichia coli (1988) (70)
Multi-resolution simulation of biomolecular systems: a review of methodological issues. (2013) (66)
On searching neighbors in computer simulations of macromolecular systems (1984) (65)
Translational and rotational diffusion of proteins. (1994) (64)
Assessing the effect of conformational averaging on the measured values of observables (2001) (62)
Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site (2005) (62)
Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation. (2005) (58)
The high-resolution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from nuclear magnetic resonance nuclear Overhauser effect data. (1994) (58)
Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. (2006) (58)
On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase. (2011) (57)
Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. (1995) (57)
An NMR‐based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution (1989) (57)
A method for constrained energy minimization of macromolecules (1980) (57)
Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time. (2005) (57)
Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. (2006) (55)
Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. (2002) (54)
Biomolecular simulation: historical picture and future perspectives. (2008) (52)
Fibrillation power, an alternative method of ECG spectral analysis for prediction of countershock success in a porcine model of ventricular fibrillation. (2001) (50)
On the similarity of properties in solution or in the crystalline state: A molecular dynamics study of hen lysozyme (2000) (50)
The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures (2007) (49)
Determination of protein structures from nuclear magnetic resonance data using a restrained molecular dynamics approach: the lac repressor DNA binding domain. (1985) (49)
Calculation of the Redox Potential of the Protein Azurin and Some Mutants (2005) (49)
On the occurrence of three-center hydrogen bonds in cyclodextrins in crystalline form and in aqueous solution: comparison of neutron diffraction and molecular dynamics results. (1988) (49)
Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands. (2007) (48)
Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen: The Effect of Explicitly Including Solvent Polarization. (2007) (48)
Methane clustering in explicit water: effect of urea on hydrophobic interactions. (2005) (47)
Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water. (2007) (46)
Molecular dynamics: perspective for complex systems. (1982) (46)
Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm (1993) (45)
Molecular dynamics simulations of the holo and apo forms of retinol binding protein. Structural and dynamical changes induced by retinol removal. (1986) (45)
Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS). (2009) (45)
A Combined Solid‐State NMR and MD Characterization of the Stability and Dynamics of the HET‐s(218‐289) Prion in its Amyloid Conformation (2009) (45)
Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations (2012) (44)
Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study. (2004) (43)
Acetonitrile revisited: a molecular dynamics study of the liquid phase (2006) (43)
Prediction of the activity and stability effects of site-directed mutagenesis on a protein core. (1992) (42)
Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters. (2007) (41)
Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. (2011) (41)
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding. (2006) (41)
Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long‐time molecular dynamics simulations (1995) (41)
Unfolded state of peptides. (2002) (39)
Energy-entropy compensation in the transfer of nonpolar solutes from water to cosolvent/water mixtures. (2004) (39)
Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. (1994) (38)
On the Calculation of Atomic Forces in Classical Simulation Using the Charge-on-Spring Method To Explicitly Treat Electronic Polarization. (2007) (38)
On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperature protein unfolding simulations. (2000) (38)
Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin. (1999) (37)
Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water. (2012) (37)
Are NMR-derived model structures for beta-peptides representative for the ensemble of structures adopted in solution? (2004) (37)
Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. (2001) (37)
Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study. (1991) (37)
Temperature and urea induced denaturation of the TRP‐cage mini protein TC5b: A simulation study consistent with experimental observations (2009) (35)
Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations. (2005) (35)
Sampling of rare events using hidden restraints. (2006) (35)
Atomic models of de novo designed cc beta-Met amyloid-like fibrils. (2008) (34)
Molecular dynamics simulations of small peptides: can one derive conformational preferences from ROESY spectra? (2003) (34)
Protein under pressure: Molecular dynamics simulation of the arc repressor (2006) (34)
Molecular‐dynamics simulation of the β domain of metallothionein with a semi‐empirical treatment of the metal core (2000) (33)
Conformational study of an Aib-rich peptide in DMSO by NMR. (2001) (33)
Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system. (2012) (33)
Current computer modeling cannot explain why two highly similar sequences fold into different structures. (2011) (32)
Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations. (1997) (32)
Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents. (2006) (32)
Simultaneous refinement of the structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals. (1994) (31)
Backbone folding of the polypeptide cardiac stimulant anthopleurin‐A determined by nuclear magnetic resonance, distance geometry and molecular dynamics (1988) (31)
Characterization of the denaturation of human α‐lactalbumin in urea by molecular dynamics simulations (2004) (31)
Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid‐binding protein (2002) (31)
Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A. (2009) (31)
A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints. (1994) (31)
The combined use of NMR, distance geometry, and restrained molecular dynamics for the conformational study of a cyclic somatostatin analogue (1988) (30)
Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: Pathway prediction and reconciliation of X‐ray crystallographic and NMR solution data (2006) (30)
Cooperative effects in the transport of small molecules through an amorphous polymer matrix. (1993) (29)
Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code (2013) (28)
Force-field dependence of the conformational properties of α,ω-dimethoxypolyethylene glycol (2009) (28)
An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. (2011) (27)
A method to explore protein side chain conformational variability using experimental data. (2009) (27)
Amine hydration: a united-atom force-field solution. (2005) (27)
Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin. (2005) (27)
Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions. (2006) (27)
Dynamical structure of carboxypeptidase A. (1989) (26)
Accessibility and order of water sites in and around proteins: A crystallographic time‐averaging study (1999) (25)
β‐Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution (2004) (25)
On using time-averaging restraints in molecular dynamics simulation (1998) (25)
Increasing the Time Step and Efficiency of Molecular Dynamics Simulations: Optimal Solutions for Equilibrium Simulations or Structure Refinement of Large Biomolecules (2003) (25)
Molecular dynamics simulation of n-dodecyl phosphate aggregate structures (2001) (25)
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides (2002) (24)
Deriving Structural Information from Experimentally Measured Data on Biomolecules. (2016) (24)
A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase (2002) (24)
Molecular dynamics simulation of lipid bilayers with GROMOS96: Application of surface tension (2005) (24)
Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system. (1995) (23)
Investigation of protein unfolding and stability by computer simulation. (1995) (22)
Fundamentals of drug design from a biophysical viewpoint (1994) (22)
Rapid non-empirical approaches for estimating relative binding free energies. (1995) (22)
Prediction of folding equilibria of differently substituted peptides using one-step perturbation. (2010) (22)
The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers. (2001) (21)
Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA. (2007) (21)
Exploring the role of the solvent in the denaturation of a protein: a molecular dynamics study of the DNA binding domain of the 434 repressor. (1995) (21)
Conformational analysis of a cyclic thymopoietin-analogue by 1H n.m.r. spectroscopy and restrained molecular dynamics simulations. (2009) (21)
Molecular dynamics simulations highlight mobile regions in proteins: A novel suggestion for converting a murine V(H) domain into a more tractable species. (2000) (21)
Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA. (2010) (20)
QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians. (2008) (20)
Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations (2005) (20)
A refined, efficient mean solvation force model that includes the interior volume contribution. (2011) (20)
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations (2012) (20)
The effect of using a polarizable solvent model upon the folding equilibrium of different β-peptides (2011) (20)
An improved simple polarisable water model for use in biomolecular simulation. (2014) (20)
Carbopeptoid folding: effects of stereochemistry, chain length, and solvent. (2004) (19)
Thirty-five years of biomolecular simulation: development of methodology, force fields and software (2012) (19)
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. (2012) (19)
Folding and Unfolding of Two Mixed α/β Peptides (2009) (19)
On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices. (2011) (19)
Interpreting experimental data by using molecular simulation instead of model building. (2009) (18)
Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques (1994) (18)
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation study. (2012) (18)
On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study. (2005) (17)
Principles of carbopeptoid folding: a molecular dynamics simulation study (2005) (17)
An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations. (2005) (17)
Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation. (2010) (17)
Orientation and conformational preference of leucine-enkephalin at the surface of a hydrated dimyristoylphosphatidylcholine bilayer: NMR and MD simulation. (2006) (16)
Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase. (2008) (16)
Simulating the Physiological Phase of Hydrated DPPC Bilayers: The Ester Moiety (2004) (16)
Disulfide bond shuffling in bovine alpha-lactalbumin: MD simulation confirms experiment. (2008) (16)
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins (2006) (16)
Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations. (2008) (16)
Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer. (2005) (15)
A one-site polarizable model for liquid chloroform: COS/C (2010) (14)
Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding (2003) (14)
beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. (2000) (14)
Helical content of a β(3)-octapeptide in methanol: molecular dynamics simulations explain a seeming discrepancy between conclusions derived from CD and NMR data. (2012) (14)
Rapid Sampling of Folding Equilibria of β-Peptides in Methanol Using a Supramolecular Solvent Model. (2014) (14)
Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin. (1994) (14)
Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients. (2013) (14)
A simple, efficient polarizable molecular model for liquid carbon tetrachloride (2011) (13)
Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation. (1994) (13)
Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water. (2013) (13)
The seven sins in academic behavior in the natural sciences. (2013) (13)
Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase. (2015) (13)
Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures (2011) (13)
Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibria. (2007) (13)
The role of computer simulation techniques in protein engineering. (1988) (12)
Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation (2002) (12)
Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study. (2004) (12)
Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution. (2012) (12)
Exploring the trigger sequence of the GCN4 coiled‐coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements (2010) (12)
Molecular dynamics simulations of peptide fragments from hen lysozyme: insight into non-native protein conformations. (1998) (12)
Structure and fluctuations of bacteriophage T4 glutaredoxin modelled by molecular dynamics. (1990) (12)
Simulation of the substrate cavity dynamics of quercetinase. (2004) (11)
Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling. (2011) (11)
Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations. (2015) (11)
On the compatibility of polarisable and non-polarisable models for liquid water (2014) (11)
Structural changes in retinol binding protein induced by retinol removal. A molecular dynamics study. (1986) (10)
MD simulation of subtilisin BPN′ in a crystal environment (1992) (10)
Using one-step perturbation to predict the folding equilibrium of differently stereochemically substituted β-peptides. (2010) (10)
Relative free enthalpies for point mutations in two proteins with highly similar sequences but different folds. (2013) (10)
Enhanced conformational sampling using enveloping distribution sampling. (2013) (10)
Structure determination of a flexible cyclic peptide based on NMR and MD simulation 3J-coupling. (2010) (9)
On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations. (2015) (9)
The thermal isomerization of the GFP chromophore: A computational study. (2010) (9)
Can one derive the conformational preference of a beta-peptide from its CD spectrum? (2002) (9)
The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states. (2015) (9)
Exploring the Conserved Water Site and Hydration of a Coiled‐Coil Trimerisation Motif: A MD Simulation Study (2008) (8)
Influence of 63Ser phosphorylation and dephosphorylation on the structure of the stathmin helical nucleation sequence: a molecular dynamics study. (2012) (8)
Combination of Enveloping Distribution Sampling (EDS) of a Soft-Core Reference-State Hamiltonian with One-Step Perturbation to Predict the Effect of Side Chain Substitution on the Relative Stability of Right- and Left-Helical Folds of β-Peptides. (2013) (7)
Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations. (2007) (7)
Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide. (2015) (7)
Molecular mechanics and dynamics in protein design. (1987) (7)
Exploring the effect of side-chain substitutions upon the secondary structure preferences of β-peptides. (2011) (7)
Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations. (2013) (7)
Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide. (2009) (7)
A Molecular Dynamics Study of the ASC and NALP1 Pyrin Domains at Neutral and Low pH (2008) (7)
Structure prediction of subtilisin BPN' mutants using molecular dynamics methods. (1993) (6)
A Comparison of Seven Fast but Approximate Methods to Compute the Free Energy of Deprotonation for Amino Acids in Aqueous Solution (2001) (6)
GROMOS polarisable model for acetone (2016) (6)
Interpreting NMR data for beta-peptides using molecular dynamics simulations. (2005) (6)
Enhancing the configurational sampling of ions in aqueous solution using adiabatic decoupling with translational temperature scaling. (2011) (6)
Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection (2010) (6)
The effect of branched side chains on the relative stability of α- and π-helices: a combination of the enveloping distribution sampling and one-step perturbation methods† (2013) (6)
Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics. (2010) (5)
Molecular dynamics simulation of thionated hen egg white lysozyme (2012) (5)
On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues. (2020) (5)
Local and collective motions in protein dynamics. (2008) (5)
Ester‐linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation – possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold (2012) (5)
Challenge of representing entropy at different levels of resolution in molecular simulation. (2015) (5)
GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2. (2015) (4)
Switching the dipole moment for 5CB on and off (2006) (4)
A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents. (2016) (4)
On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain (2013) (4)
An effective force field for molecular dynamics simulations of dimethyl sulfone (2011) (4)
A Suite of Advanced Tutorials for the GROMOS Biomolecular Simulation Software [Article v1.0] (2020) (3)
Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations. (2020) (3)
A method for conformational sampling of loops in proteins based on adiabatic decoupling and temperature or force scaling. (2011) (3)
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. (2009) (3)
Simulation of an all-beta 3-icosapeptide containing the 20 proteinogenic side chains: effect of temperature, pH, counterions, solvent, and force field on helix stability. (2006) (3)
A molecular dynamics simulation of crystalline alpha-cyclodextrin hexahydrate. (1987) (3)
Interpretation of Seemingly Contradictory Data: Low NMR S2 Order Parameters Observed in Helices and High NMR S2 Order Parameters in Disordered Loops of the Protein hGH at Low pH. (2017) (3)
Exploring the properties of small molecule protein binding via molecular simulations: the TRSH-p53 core domain complex. (2012) (3)
Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces. (2011) (3)
Use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields. (2014) (3)
On the use of 3J-coupling NMR data to derive structural information on proteins (2021) (2)
Test of a method for sampling the internal degrees of freedom of a flexible solute molecule based on adiabatic decoupling and temperature or force scaling (2012) (2)
Structural and energetic effects of the use of polarisable water to solvate proteins (2015) (2)
Molecular dynamics simulation of despentapeptide insulin in a crystalline environment. (1988) (2)
On the pitfalls of peer review (2015) (2)
Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data. (1991) (2)
Using Complementary NMR Data Sets To Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4. (2017) (2)
Erratum: "Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system" [J. Chem. Phys. 137, 044120 (2012)]. (2017) (2)
On deriving spatial protein structure from NMR or X-ray diffraction data. (1991) (2)
On the use of one-step perturbation to investigate the dependence of different properties of liquid water on a variation of model parameters from a single simulation† (2013) (2)
Molecular dynamics simulation of the last step of a catalytic cycle: Product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis (2012) (2)
Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability (2007) (2)
Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion. (2016) (2)
Correction to "Polarizable Model for DMSO and DMSO-Water Mixtures". (2016) (1)
Herman Berendsen: Researcher, teacher, scholar, colleague, skipper (1999) (1)
On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters. (2014) (1)
Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme (2022) (1)
On the use of intra‐molecular distance and angle constraints to lengthen the time step in molecular and stochastic dynamics simulations of proteins (2021) (0)
On the calculation of 3Jαβ-coupling constants for side chains in proteins (2012) (0)
Time-averaged order parameter restraints in molecular dynamics simulations (2014) (0)
Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data (2013) (0)
A Method to Derive Structural Information on Molecules from Residual Dipolar Coupling NMR Data. (2022) (0)
On the use of one-step perturbation to investigate the dependence of NOE-derived atom–atom distance bound violations of peptides upon a variation of force-field parameters (2014) (0)
The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged. (2001) (0)
An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation (2012) (0)
Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers (2013) (0)
Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations (2015) (0)
On the use of 3J-coupling NMR data to derive structural information on proteins (2021) (0)
On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water. (2013) (0)
Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations (2012) (0)

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