Wilfred F. Van Gunsteren
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Wilfred F. Van Gunsterenphysics Degrees
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Biophysics
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Chemistry Physics
Wilfred F. Van Gunsteren's Degrees
- PhD Chemistry University of Amsterdam
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(Suggest an Edit or Addition)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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