FIND

researchers

DISCOVER

relevant articles

PROMOTE

your research

now for free

Wilfred van Gunsteren

Research Profile

Activities & Behaviors

Concepts & Ideas

Occupations

Thermodynamics

Phenomena

Chemicals & Drugs

Physiology

Protein Folding

Procedures

Genes & Molecular Sequences

Amino Acid Sequences

Co-author Network

Publications

TOP 3
Andreas P Eichenberger; Wilfred F van Gunsteren; Lorna J Smith
Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data.
Katharina Meier; Sereina Riniker; Alexandra Choutko; Jozica Dolenc; Andreas P Eichenberger; Wilfred F van Gunsteren
Multi-resolution simulation of biomolecular systems: a review of methodological issues.
Zhixiong Lin; Wilfred F van Gunsteren
On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment.

Register for free to view:

Visualized networks:

See your personal network in
sophisticated graphical views

GeoTargeted Searches:

Locate experts around the world
and connect with global collaborators

Research Profiles:

See the research activity
of experts around the globe

Geonetwork of Wilfred van Gunsteren (preview)

Cities where this author has publications
Cities where co-authors of this author have publications

Flash Player Required

All Publications

2013: Andreas P Eichenberger; Wilfred F van Gunsteren; Lorna J Smith
Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data.
Journal of biomolecular NMR 2013;55(4):339-53.
2013: Katharina Meier; Sereina Riniker; Alexandra Choutko; Jozica Dolenc; Andreas P Eichenberger; Wilfred F van Gunsteren
Multi-resolution simulation of biomolecular systems: a review of methodological issues.
Angewandte Chemie (International ed. in English) 2013;52(10):2820-34.
2013: Zhixiong Lin; Wilfred F van Gunsteren
On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment.
Journal of computational chemistry 2013;34(5):387-93.
2013: Wilfred F van Gunsteren
The seven sins in academic behavior in the natural sciences.
Angewandte Chemie (International ed. in English) 2013;52(1):118-22.
2013: Manuel M Müller; Wilfred F van Gunsteren; Jane R Allison; Laurent Gaillon; Narupat Hongdilokkul; Peter Kast; Philippe Marlière; Donald Hilvert
Directed evolution of a model primordial enzyme provides insights into the development of the genetic code.
PLoS genetics 2013;9(1):e1003187.
2012: Sereina Riniker; Andreas Steffen; Luzi J Barandun; François Diederich; Oliver Krämer; Wilfred F van Gunsteren
Free enthalpies of replacing water molecules in protein binding pockets.
Journal of computer-aided molecular design 2012;26(12):1293-309.
2012: Alexandra Choutko; Wilfred F van Gunsteren
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.
Protein science : a publication of the Protein Society 2012;21(11):1672-81.
2012: Thomas S Hofer; Wilfred F van Gunsteren
Exploring the properties of small molecule protein binding via molecular simulations: the TRSH-p53 core domain complex.
Molecular bioSystems 2012;8(11):2891-900.
2012: John H Missimer; Michel O Steinmetz; Wilfred F van Gunsteren; Jožica Dolenc
Influence of 63Ser phosphorylation and dephosphorylation on the structure of the stathmin helical nucleation sequence: a molecular dynamics study.
Biochemistry 2012;51(42):8455-63.
2012: Katharina Meier; Nathan Schmid; Wilfred F van Gunsteren
Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages.
Journal of computational chemistry 2012;33(26):2108-17.
2012: Sereina Riniker; Jane R Allison; Wilfred F van Gunsteren
On developing coarse-grained models for biomolecular simulation: a review.
Physical chemistry chemical physics : PCCP 2012;14(36):12423-30.
2012: Bruno A C Horta; Wei Huang; Zhixiong Lin; Sereina Riniker; Wilfred F van Gunsteren; Philippe H Hünenberger
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol.
Journal of computational chemistry 2012;33(24):1907-17.
2012: Dongqi Wang; Wilfred F van Gunsteren; Zhifang Chai
Recent advances in computational actinoid chemistry.
Chemical Society reviews 2012;41(17):5836-65.
2012: Zhixiong Lin; Tobias A Timmerscheidt; Wilfred F van Gunsteren
Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution.
The Journal of chemical physics 2012;137(6):064108.
2012: Sereina Riniker; Andreas P Eichenberger; Wilfred F van Gunsteren
Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water.
The journal of physical chemistry. B 2012;116(30):8873-9.
2012: Sereina Riniker; Andreas P Eichenberger; Wilfred F van Gunsteren
Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.
European biophysics journal : EBJ 2012;41(8):647-61.
2012: Wei Huang; Andreas P Eichenberger; Wilfred F van Gunsteren
Molecular dynamics simulation of thionated hen egg white lysozyme.
Protein science : a publication of the Protein Society 2012;21(8):1153-61.
2012: Sereina Riniker; Wilfred F van Gunsteren
Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system.
The Journal of chemical physics 2012;137(4):044120.
2012: Denise Steiner; Jane R Allison; Andreas P Eichenberger; Wilfred F van Gunsteren
On the calculation of ³Jαβ-coupling constants for side chains in proteins.
Journal of biomolecular NMR 2012;53(3):223-46.
2012: Denise Steiner; Wilfred F van Gunsteren
An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.
European biophysics journal : EBJ 2012;41(7):579-95.
2012: Denise Steiner; Chris Oostenbrink; Wilfred F van Gunsteren
Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9.
Journal of computational chemistry 2012;33(17):1467-77.
2012: Sereina Riniker; Bram Thijssen; Wilfred F van Gunsteren; Saumya Gupta; Bruno A C Horta; Philippe H Hünenberger
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: a molecular dynamics simulation study.
Chemphyschem : a European journal of chemical physics and physical chemistry 2012;13(5):1182-90.
2012: Niels Hansen; Matthias Knecht; Sereina Riniker; Jozica Dolenc; Wilfred F van Gunsteren
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution.
Journal of computational chemistry 2012;33(6):640-51.
2012: Jane R Allison; Sereina Riniker; Wilfred F van Gunsteren
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol.
The Journal of chemical physics 2012;136(5):054505.
2011: Alexandra Choutko; Wilfred F van Gunsteren; Philippe H Hünenberger
Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces.
Chemphyschem : a European journal of chemical physics and physical chemistry 2011;12(17):3214-23.
2011: Sereina Riniker; Denise Steiner; Clara D Christ; Halvor S Hansen; Philippe H Hünenberger; Chris Oostenbrink; Wilfred F van Gunsteren
Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.
The journal of physical chemistry. B 2011;115(46):13570-7.
2011: Zhixiong Lin; Wilfred F van Gunsteren
Exploring the effect of side-chain substitutions upon the secondary structure preferences of β-peptides.
The journal of physical chemistry. B 2011;115(44):12984-92.
2011: Nathan Schmid; Jane R Allison; Jozica Dolenc; Andreas P Eichenberger; Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Biomolecular structure refinement using the GROMOS simulation software.
Journal of biomolecular NMR 2011;51(3):265-81.
2011: Anna-Pitschna E Kunz; Wilfred F van Gunsteren
A method for conformational sampling of loops in proteins based on adiabatic decoupling and temperature or force scaling.
Chemphyschem : a European journal of chemical physics and physical chemistry 2011;12(14):2609-14.
2011: Anna-Pitschna E Kunz; Haiyan Liu; Wilfred F van Gunsteren
Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling.
The Journal of chemical physics 2011;135(10):104106.
2011: Antonija Kuzmanic; Navraj S Pannu; Wilfred F van Gunsteren; Daniela Kruschel; Bojan Zagrovic
Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures.
Journal of molecular biology 2011;411(1):286-97.
2011: Jozica Dolenc; Roberto Gaspari; Sereina Riniker; Xavier Daura; Wilfred F van Gunsteren
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.
Journal of computer-aided molecular design 2011;25(8):709-16.
2011: Denise Steiner; Chris Oostenbrink; François Diederich; Martina Zürcher; Wilfred F van Gunsteren
Calculation of binding free energies of inhibitors to plasmepsin II.
Journal of computational chemistry 2011;32(9):1801-12.
2011: Sereina Riniker; Clara D Christ; Niels Hansen; Alan E Mark; Pramod C Nair; Wilfred F van Gunsteren
Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.
The Journal of chemical physics 2011;135(2):024105.
2011: Nathan Schmid; Moritz Winger; Alexandra Choutko; Andreas P Eichenberger; Alan E Mark; Sereina Riniker; Wilfred F van Gunsteren
Definition and testing of the GROMOS force-field versions 54A7 and 54B7.
European biophysics journal : EBJ 2011;40(7):843-56.
2011: Jane R Allison; Katharina Boguslawski; Franca Fraternali; Wilfred F van Gunsteren
A refined, efficient mean solvation force model that includes the interior volume contribution.
The journal of physical chemistry. B 2011;115(15):4547-57.
2011: Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Enhancing the configurational sampling of ions in aqueous solution using adiabatic decoupling with translational temperature scaling.
The journal of physical chemistry. B 2011;115(12):2931-6.
2011: Sereina Riniker; Wilfred F van Gunsteren
A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.
The Journal of chemical physics 2011;134(8):084110.
2011: Alexandra Choutko; Alice Glättli; César Fernández; Christian Hilty; Kurt Wüthrich; Wilfred F van Gunsteren
Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle.
European biophysics journal : EBJ 2011;40(1):39-58.
2010: Zhixiong Lin; Wilfred F van Gunsteren
Using one-step perturbation to predict the folding equilibrium of differently stereochemically substituted β-peptides.
Physical chemistry chemical physics : PCCP 2010;12(47):15442-7.
2010: John H Missimer; Jožica Dolenc; Michel O Steinmetz; Wilfred F van Gunsteren
Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements.
Protein science : a publication of the Protein Society 2010;19(12):2462-74.
2010: Jane R Allison; Marlen Müller; Wilfred F van Gunsteren
A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability.
Protein science : a publication of the Protein Society 2010;19(11):2186-95.
2010: Zhixiong Lin; Haiyan Liu; Wilfred F van Gunsteren
Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution.
Journal of computational chemistry 2010;31(13):2419-27.
2010: Dongqi Wang; Thomas Merz; Wilfred F van Gunsteren
The thermal isomerization of the GFP chromophore: A computational study.
Physical chemistry chemical physics : PCCP 2010;12(36):11051-61.
2010: Jozica Dolenc; Sarah Gerster; Wilfred F van Gunsteren
Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA.
The journal of physical chemistry. B 2010;114(34):11164-72.
2010: Jane R Allison; Gian-Peider Moll; Wilfred F van Gunsteren
Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation.
Biochemistry 2010;49(32):6916-27.
2010: Jozica Dolenc; John H Missimer; Michel O Steinmetz; Wilfred F van Gunsteren
Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.
Journal of biomolecular NMR 2010;47(3):221-35.
2010: Zhixiong Lin; Jörgen Kornfeld; Markus Mächler; Wilfred F van Gunsteren
Prediction of folding equilibria of differently substituted peptides using one-step perturbation.
Journal of the American Chemical Society 2010;132(21):7276-8.
2010: Nathan Schmid; Mathias Bötschi; Wilfred F van Gunsteren
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.
Journal of computational chemistry 2010;31(8):1636-43.
2010: Clara D Christ; Alan E Mark; Wilfred F van Gunsteren
Basic ingredients of free energy calculations: a review.
Journal of computational chemistry 2010;31(8):1569-82.
2010: Bettina G. Keller; Zrinka Gattin; Wilfred F van Gunsteren
What stabilizes the 3(14)-helix in beta3-peptides? A conformational analysis using molecular simulation.
Proteins 2010;78(7):1677-90.
2010: David Poger; Wilfred F van Gunsteren; Alan E Mark
A new force field for simulating phosphatidylcholine bilayers.
Journal of computational chemistry 2010;31(6):1117-25.
2010: Zrinka Gattin; Judith Zaugg; Wilfred F van Gunsteren
Structure determination of a flexible cyclic peptide based on NMR and MD simulation 3J-coupling.
Chemphyschem : a European journal of chemical physics and physical chemistry 2010;11(4):830-5.
2010: Bettina G. Keller; Xavier Daura; Wilfred F van Gunsteren
Comparing geometric and kinetic cluster algorithms for molecular simulation data.
The Journal of chemical physics 2010;132(7):074110.
2010: Katharina Meier; Wilfred F van Gunsteren
Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics.
The journal of physical chemistry. A 2010;114(4):1852-9.
2009: Jane R Allison; Wilfred F van Gunsteren
A method to explore protein side chain conformational variability using experimental data.
Chemphyschem : a European journal of chemical physics and physical chemistry 2009;10(18):3213-28.
2009: Beat Vögeli; Takuya F Segawa; Dominik Leitz; Alexander Sobol; Alexandra Choutko; Daniel Trzesniak; Wilfred F van Gunsteren; Roland Riek
Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups.
Journal of the American Chemical Society 2009;131(47):17215-25.
2009: Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D.
The journal of physical chemistry. A 2009;113(43):11570-9.
2009: Z Gattin; S Riniker; P J Hore; K Hun Mok; Wilfred F van Gunsteren
Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations.
Protein science : a publication of the Protein Society 2009;18(10):2090-9.
2009: Dongqi Wang; Bernhard Jaun; Wilfred F van Gunsteren
Folding and unfolding of two mixed alpha/beta peptides.
Chembiochem : a European journal of chemical biology 2009;10(12):2032-41.
2009: Clara D Christ; Wilfred F van Gunsteren
Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.
Journal of computational chemistry 2009;30(11):1664-79.
2009: Adam Lange; Zrinka Gattin; Hélène Van Melckebeke; Christian Wasmer; Alice Soragni; Wilfred F van Gunsteren; Beat H Meier
A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation.
Chembiochem : a European journal of chemical biology 2009;10(10):1657-65.
2009: Zrinka Gattin; Wilfred F van Gunsteren
Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide.
The journal of physical chemistry. B 2009;113(25):8695-703.
2009: Zrinka Gattin; Julian Schwartz; Raveendra I Mathad; Bernhard Jaun; Wilfred F van Gunsteren
Interpreting experimental data by using molecular simulation instead of model building.
Chemistry (Weinheim an der Bergstrasse, Germany) 2009;15(26):6389-98.
2009: Christian L Müller; Ivo F Sbalzarini; Wilfred F van Gunsteren; Bojan Zagrović; Philippe H Hünenberger
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.
The Journal of chemical physics 2009;130(21):214904.
2009: Moritz Winger; Daniel Trzesniak; Riccardo Baron; Wilfred F van Gunsteren
On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models.
Physical chemistry chemical physics : PCCP 2009;11(12):1934-41.
2009: Daan P Geerke; Sandra Luber; Koni H Marti; Wilfred F van Gunsteren
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase.
Journal of computational chemistry 2009;30(4):514-23.
2008: Nathan Schmid; Christine Bolliger; Lorna J Smith; Wilfred F van Gunsteren
Disulfide bond shuffling in bovine alpha-lactalbumin: MD simulation confirms experiment.
Biochemistry 2008;47(46):12104-7.
2008: Jozica Dolenc; Riccardo Baron; John H Missimer; Michel O Steinmetz; Wilfred F van Gunsteren
Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.
Chembiochem : a European journal of chemical biology 2008;9(11):1749-56.
2008: Bojan Zagrovic; Zrinka Gattin; Justin Kai-Chi Lau; Matthias Huber; Wilfred F van Gunsteren
Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment.
European biophysics journal : EBJ 2008;37(6):903-12.
2008: Clara D Christ; Wilfred F van Gunsteren
Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions.
The Journal of chemical physics 2008;128(17):174112.
2008: Zrinka Gattin; Wilfred F van Gunsteren
A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pH.
Chembiochem : a European journal of chemical biology 2008;9(6):923-33.
2008: Wilfred F van Gunsteren; Jozica Dolenc; Alan E Mark
Molecular simulation as an aid to experimentalists.
Current opinion in structural biology 2008;18(2):149-53.
2008: Fabienne Schwab; Wilfred F van Gunsteren; Bojan Zagrovic
Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase.
Biochemistry 2008;47(9):2945-51.
2008: Michel O Steinmetz; Zrinka Gattin; rene verel; Barbara Ciani; Thusnelda Stromer; Janelle M Green; Peter Tittmann; Clemens Schulze-Briese; Heinz Gross; Wilfred F van Gunsteren; Beat H Meier; Louise C Serpell; Shirley A Müller; Richard A Kammerer
Atomic models of de novo designed cc beta-Met amyloid-like fibrils.
Journal of molecular biology 2008;376(3):898-912.
2008: Wilfred F van Gunsteren; Jozica Dolenc
Biomolecular simulation: historical picture and future perspectives.
Biochemical Society transactions 2008;36(Pt 1):11-5.
2008: Markus Christen; Wilfred F van Gunsteren
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.
Journal of computational chemistry 2008;29(2):157-66.
2008: Daan P Geerke; Stephan Thiel; Walter Thiel; Wilfred F van Gunsteren
QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians.
Physical chemistry chemical physics : PCCP 2008;10(2):297-302.
2008: Ricard Boned; Wilfred F van Gunsteren; Xavier Daura
Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.
Chemistry (Weinheim an der Bergstrasse, Germany) 2008;14(16):5039-46.
2007: Markus Christen; Bettina G. Keller; Wilfred F van Gunsteren
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.
Journal of biomolecular NMR 2007;39(4):265-73.
2007: Michel A Cuendet; Wilfred F van Gunsteren
On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm.
The Journal of chemical physics 2007;127(18):184102.
2007: Markus Christen; Clara D Christ; Wilfred F van Gunsteren
Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations.
Chemphyschem : a European journal of chemical physics and physical chemistry 2007;8(10):1557-64.
2007: David B Kony; Wolfgang Damm; Serge Stoll; Wilfred F van Gunsteren; Philippe H Hünenberger
Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water.
Biophysical journal 2007;93(2):442-55.
2007: John H Missimer; Michel O Steinmetz; Riccardo Baron; Fritz K Winkler; Richard A Kammerer; Xavier Daura; Wilfred F van Gunsteren
Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.
Protein science : a publication of the Protein Society 2007;16(7):1349-59.
2007: Daan P Geerke; Wilfred F van Gunsteren
Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
The journal of physical chemistry. B 2007;111(23):6425-36.
2007: Nathan Schmid; Bojan Zagrovic; Wilfred F van Gunsteren
Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA.
Biochemistry 2007;46(22):6500-12.
2007: David B Kony; Philippe H Hünenberger; Wilfred F van Gunsteren
Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics.
Protein science : a publication of the Protein Society 2007;16(6):1101-18.
2007: Clara D Christ; Wilfred F van Gunsteren
Enveloping distribution sampling: a method to calculate free energy differences from a single simulation.
The Journal of chemical physics 2007;126(18):184110.
2007: Zrinka Gattin; Alice Glättli; Bernhard Jaun; Wilfred F van Gunsteren
Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibria.
Biopolymers 2007;85(4):318-32.
2007: Riccardo Baron; Daniel Trzesniak; André H M de Vries; Andreas Elsener; Siewert J Marrink; Wilfred F van Gunsteren
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Chemphyschem : a European journal of chemical physics and physical chemistry 2007;8(3):452-61.
2007: Daniel Trzesniak; Anna-Pitschna E Kunz; Wilfred F van Gunsteren
A comparison of methods to compute the potential of mean force.
Chemphyschem : a European journal of chemical physics and physical chemistry 2007;8(1):162-9.
2007: Bettina G. Keller; Markus Christen; Chris Oostenbrink; Wilfred F van Gunsteren
On using oscillating time-dependent restraints in MD simulation.
Journal of biomolecular NMR 2007;37(1):1-14.
2006: Daniel Trzesniak; Bernhard Jaun; Raveendra I Mathad; Wilfred F van Gunsteren
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.
Biopolymers 2006;83(6):636-45.
2006: Lorna J Smith; Robert J Davies; Wilfred F van Gunsteren
Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: comparisons of the wild-type protein, a b-type variant, and the apo state.
Proteins 2006;65(3):702-11.
2006: Daniel Trzesniak; Wilfred F van Gunsteren
Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data.
Protein science : a publication of the Protein Society 2006;15(11):2544-51.
2006: Haibo Yu; Andreas Kohl; H Kaspar Binz; Andreas Plückthun; Markus G Grütter; Wilfred F van Gunsteren
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins.
Proteins 2006;65(2):285-95.
2006: Daniel Trzesniak; Roberto D Lins; Wilfred F van Gunsteren
Protein under pressure: molecular dynamics simulation of the arc repressor.
Proteins 2006;65(1):136-44.
2006: Haibo Yu; Daan P Geerke; Haiyan Liu; Wilfred F van Gunsteren
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.
Journal of computational chemistry 2006;27(13):1494-504.
2006: Jozica Dolenc; Riccardo Baron; Chris Oostenbrink; Joze Koller; Wilfred F van Gunsteren
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.
Biophysical journal 2006;91(4):1460-70.
2006: Riccardo Baron; André H M de Vries; Philippe H Hünenberger; Wilfred F van Gunsteren
Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations.
The journal of physical chemistry. B 2006;110(31):15602-14.
2006: Nico F A van der Vegt; Maeng-Eun Lee; Daniel Trzesniak; Wilfred F van Gunsteren
Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions.
The journal of physical chemistry. B 2006;110(26):12852-5.
2006: Wilfred F van Gunsteren; Dirk Bakowies; Riccardo Baron; Indira Chandrasekhar; Markus Christen; Xavier Daura; Peter Gee; Daan P Geerke; Alice Glättli; Philippe H Hünenberger; Mika A Kastenholz; Chris Oostenbrink; Merijn Schenk; Daniel Trzesniak; Nico F A van der Vegt; Haibo B Yu
Biomolecular modeling: Goals, problems, perspectives.
Angewandte Chemie (International ed. in English) 2006;45(25):4064-92.
2006: Cristina S Pereira; David B Kony; Riccardo Baron; Martin Müller; Wilfred F van Gunsteren; Philippe H Hünenberger
Conformational and dynamical properties of disaccharides in water: a molecular dynamics study.
Biophysical journal 2006;90(12):4337-44.
2006: Yu Zhou; Chris Oostenbrink; Aldo Jongejan; Wilfred F van Gunsteren; Wilfred R Hagen; Simon W De Leeuw; Jaap A Jongejan
Computational study of ground-state chiral induction in small peptides: comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations.
Journal of computational chemistry 2006;27(7):857-67.
2006: Markus Christen; Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Sampling of rare events using hidden restraints.
The journal of physical chemistry. B 2006;110(16):8488-98.
2006: Riccardo Baron; André H M de Vries; Philippe H Hünenberger; Wilfred F van Gunsteren
Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates.
The journal of physical chemistry. B 2006;110(16):8464-73.
2006: Markus Christen; Wilfred F van Gunsteren
Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.
The Journal of chemical physics 2006;124(15):154106.
2006: Peter J Gee; Wilfred F van Gunsteren
Terminal-group effects on the folding behavior of selected beta-peptides.
Proteins 2006;63(1):136-43.
2006: Bojan Zagrovic; Wilfred F van Gunsteren
Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
Proteins 2006;63(1):210-8.
2006: Daan P Geerke; Wilfred F van Gunsteren
Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents.
Chemphyschem : a European journal of chemical physics and physical chemistry 2006;7(3):671-8.
2006: Alice Glättli; Indira Chandrasekhar; Wilfred F van Gunsteren
A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer.
European biophysics journal : EBJ 2006;35(3):255-67.
2006: Indira Chandrasekhar; Wilfred F van Gunsteren; Giorgia Zandomeneghi; Philip Williamson; Beat H Meier
Orientation and conformational preference of leucine-enkephalin at the surface of a hydrated dimyristoylphosphatidylcholine bilayer: NMR and MD simulation.
Journal of the American Chemical Society 2006;128(1):159-70.
2005: Peter J Gee; Wilfred F van Gunsteren
Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer.
Chemistry (Weinheim an der Bergstrasse, Germany) 2005;12(1):72-5.
2005: Alice Glättli; Xavier Daura; Pascal Bindschädler; Bernhard Jaun; Yogesh Mahajan; Raveendra I Mathad; Magnus Rueping; Dieter Seebach; Wilfred F van Gunsteren
On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study.
Chemistry (Weinheim an der Bergstrasse, Germany) 2005;11(24):7276-93.
2005: Markus Christen; Philippe H Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P Geerke; Tim N Heinz; Mika A Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; Wilfred F van Gunsteren
The GROMOS software for biomolecular simulation: GROMOS05.
Journal of computational chemistry 2005;26(16):1719-51.
2005: Daniel Trzesniak; Alice Glättli; Bernhard Jaun; Wilfred F van Gunsteren
Interpreting NMR data for beta-peptides using molecular dynamics simulations.
Journal of the American Chemical Society 2005;127(41):14320-9.
2005: Chris Oostenbrink; Daniel Juchli; Wilfred F van Gunsteren
Amine hydration: a united-atom force-field solution.
Chemphyschem : a European journal of chemical physics and physical chemistry 2005;6(9):1800-4.
2005: Bojan Zagrovic; Jan Lipfert; Eric J Sorin; Ian S Millett; Wilfred F van Gunsteren; Sebastian Doniach; Vijay S Pande
Unusual compactness of a polyproline type II structure.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(33):11698-703.
2005: John H Missimer; Michel O Steinmetz; Wolfgang Jahnke; Fritz K Winkler; Wilfred F van Gunsteren; Xavier Daura
Molecular-dynamics simulations of C- and N-terminal peptide derivatives of GCN4-p1 in aqueous solution.
Chemistry & biodiversity 2005;2(8):1086-104.
2005: Chris Oostenbrink; Wilfred F van Gunsteren
Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations.
Chemistry (Weinheim an der Bergstrasse, Germany) 2005;11(15):4340-8.
2005: André H M de Vries; Indira Chandrasekhar; Wilfred F van Gunsteren; Philippe H Hünenberger
Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time.
The journal of physical chemistry. B 2005;109(23):11643-52.
2005: Chris Oostenbrink; Thereza A Soares; Nico F A van der Vegt; Wilfred F van Gunsteren
Validation of the 53A6 GROMOS force field.
European biophysics journal : EBJ 2005;34(4):273-84.
2005: Chris Oostenbrink; Wilfred F van Gunsteren
Free energies of ligand binding for structurally diverse compounds.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6750-4.
2005: Thereza A Soares; Philippe H Hünenberger; Mika A Kastenholz; Vincent Kräutler; Thomas Lenz; Roberto D Lins; Chris Oostenbrink; Wilfred F van Gunsteren
An improved nucleic acid parameter set for the GROMOS force field.
Journal of computational chemistry 2005;26(7):725-37.
2005: Markus Christen; Wilfred F van Gunsteren
An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations.
The Journal of chemical physics 2005;122(14):144106.
2005: Vincent Kräutler; Andreas Aemissegger; Philippe H Hünenberger; Donald Hilvert; Tomas Hansson; Wilfred F van Gunsteren
Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin.
Journal of the American Chemical Society 2005;127(13):4935-42.
2005: Marieke van den Bosch; Marcel Swart; Jaap G Snijders; Herman J C Berendsen; Alan E Mark; Chris Oostenbrink; Wilfred F van Gunsteren; Gerard W Canters
Calculation of the redox potential of the protein azurin and some mutants.
Chembiochem : a European journal of chemical biology 2005;6(4):738-46.
2005: Andreas Aemissegger; Vincent Kräutler; Wilfred F van Gunsteren; Donald Hilvert
A photoinducible beta-hairpin.
Journal of the American Chemical Society 2005;127(9):2929-36.
2005: Riccardo Baron; Dirk Bakowies; Wilfred F van Gunsteren
Principles of carbopeptoid folding: a molecular dynamics simulation study.
Journal of peptide science : an official publication of the European Peptide Society 2005;11(2):74-84.
2005: Lorna J Smith; Rachel M Jones; Wilfred F van Gunsteren
Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations.
Proteins 2005;58(2):439-49.
2005: Chris Oostenbrink; Wilfred F van Gunsteren
Methane clustering in explicit water: effect of urea on hydrophobic interactions.
Physical chemistry chemical physics : PCCP 2005;7(1):53-8.
2005: Jozica Dolenc; Chris Oostenbrink; Joze Koller; Wilfred F van Gunsteren
Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site.
Nucleic acids research 2005;33(2):725-33.
2005: Shang-Te Danny Hsu; Christine Peter; Wilfred F van Gunsteren; Alexandre Bonvin
Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation.
Biophysical journal 2005;88(1):15-24.
2004: Thereza A Soares; Xavier Daura; Chris Oostenbrink; L J Smith; Wilfred F van Gunsteren
Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.
Journal of biomolecular NMR 2004;30(4):407-22.
2004: Marieke van den Bosch; Marcel Swart; Wilfred F van Gunsteren; Gerard W Canters
Simulation of the substrate cavity dynamics of quercetinase.
Journal of molecular biology 2004;344(3):725-38.
2004: Alice Glättli; Wilfred F van Gunsteren
Are NMR-derived model structures for beta-peptides representative for the ensemble of structures adopted in solution?
Angewandte Chemie (International ed. in English) 2004;43(46):6312-6.
2004: Haibo Yu; Wilfred F van Gunsteren
Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice.
The Journal of chemical physics 2004;121(19):9549-64.
2004: Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.
Journal of computational chemistry 2004;25(13):1656-76.
2004: Clara M Santiveri; M Angeles Jiménez; Manuel Rico; Wilfred F van Gunsteren; Xavier Daura
beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.
Journal of peptide science : an official publication of the European Peptide Society 2004;10(9):546-65.
2004: Riccardo Baron; Dirk Bakowies; Wilfred F van Gunsteren
Carbopeptoid folding: effects of stereochemistry, chain length, and solvent.
Angewandte Chemie (International ed. in English) 2004;43(31):4055-9.
2004: Haibo Yu; Manfred Amann; Tomas Hansson; Jutta Köhler; Günter Wich; Wilfred F van Gunsteren
Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study.
Carbohydrate research 2004;339(10):1697-709.
2004: Haibo Yu; Maaike Ramseier; Roland Bürgi; Wilfred F van Gunsteren
Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study.
Chemphyschem : a European journal of chemical physics and physical chemistry 2004;5(5):633-41.
2004: Sofía Calero; Santiago Lago; Wilfred F van Gunsteren; Xavier Daura
Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulation.
Chemistry & biodiversity 2004;1(3):505-19.
2004: Christine Peter; Chris Oostenbrink; Arthur van Dorp; Wilfred F van Gunsteren
Estimating entropies from molecular dynamics simulations.
The Journal of chemical physics 2004;120(6):2652-61.
2004: Chris Oostenbrink; Wilfred F van Gunsteren
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation.
Proteins 2004;54(2):237-46.
2004: Nico F A van der Vegt; Daniel Trzesniak; Besnik Kasumaj; Wilfred F van Gunsteren
Energy-entropy compensation in the transfer of nonpolar solutes from water to cosolvent/water mixtures.
Chemphyschem : a European journal of chemical physics and physical chemistry 2004;5(1):144-7.
2004: Haibo Yu; Xavier Daura; Wilfred F van Gunsteren
Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding.
Proteins 2004;54(1):116-27.
2003: Christine Peter; Magnus Rueping; Hans Jakob Wörner; Bernhard Jaun; Dieter Seebach; Wilfred F van Gunsteren
Molecular dynamics simulations of small peptides: can one derive conformational preferences from ROESY spectra?
Chemistry (Weinheim an der Bergstrasse, Germany) 2003;9(23):5838-49.
2003: Xavier Daura; Dirk Bakowies; Dieter Seebach; Jörg Fleischhauer; Wilfred F van Gunsteren; Peter Krüger
Circular dichroism spectra of beta-peptides: sensitivity to molecular structure and effects of motional averaging.
European biophysics journal : EBJ 2003;32(8):661-70.
2003: Chris Oostenbrink; Wilfred F van Gunsteren
Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character.
Journal of computational chemistry 2003;24(14):1730-9.
2003: Alice Glättli; Xavier Daura; Wilfred F van Gunsteren
A novel approach for designing simple point charge models for liquid water with three interaction sites.
Journal of computational chemistry 2003;24(9):1087-96.
2003: Indira Chandrasekhar; Mika A Kastenholz; Roberto D Lins; Chris Oostenbrink; Lukas D Schuler; D Peter Tieleman; Wilfred F van Gunsteren
A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field.
European biophysics journal : EBJ 2003;32(1):67-77.
2002: Iris Antes; Walter Thiel; Wilfred F van Gunsteren
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.
European biophysics journal : EBJ 2002;31(7):504-20.
2002: David B Kony; W Damm; S Stoll; Wilfred F van Gunsteren
An improved OPLS-AA force field for carbohydrates.
Journal of computational chemistry 2002;23(15):1416-29.
2002: Alice Glättli; Xavier Daura; Dieter Seebach; Wilfred F van Gunsteren
Can one derive the conformational preference of a beta-peptide from its CD spectrum?
Journal of the American Chemical Society 2002;124(44):12972-8.
2002: Lorna J Smith; Xavier Daura; Wilfred F van Gunsteren
Assessing equilibration and convergence in biomolecular simulations.
Proteins 2002;48(3):487-96.
2002: Regula Walser; Philippe H Hünenberger; Wilfred F van Gunsteren
Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells.
Proteins 2002;48(2):327-40.
2002: K Anton Feenstra; Christine Peter; Ruud M Scheek; Wilfred F van Gunsteren; Alan E Mark
A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides.
Journal of biomolecular NMR 2002;23(3):181-94.
2002: Dirk Bakowies; Wilfred F van Gunsteren
Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein.
Proteins 2002;47(4):534-45.
2002: Roland Bürgi; Peter A Kollman; Wilfred F van Gunsteren
Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.
Proteins 2002;47(4):469-80.
2002: Indira Chandrasekhar; Wilfred F van Gunsteren
A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase.
European biophysics journal : EBJ 2002;31(2):89-101.
2002: Fred A Hamprecht; Walter Thiel; Wilfred F van Gunsteren
Chemical library subset selection algorithms: a unified derivation using spatial statistics.
Journal of chemical information and computer sciences 2002;42(2):414-28.
2002: Heiko Schäfer; Lorna J Smith; Alan E Mark; Wilfred F van Gunsteren
Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin.
Proteins 2002;46(2):215-24.
2002: Dirk Bakowies; Wilfred F van Gunsteren
Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water.
Journal of molecular biology 2002;315(4):713-36.
2002: Xavier Daura; Alice Glättli; Peter Gee; Christine Peter; Wilfred F van Gunsteren
Unfolded state of peptides.
Advances in protein chemistry 2002;62():341-60.
2001: Fred A Hamprecht; Ulrich Achleitner; Anette C Krismer; Karl H Lindner; Volker Wenzel; Hans-Ulrich Strohmenger; W Thiel; Wilfred F van Gunsteren; Anton Amann
Fibrillation power, an alternative method of ECG spectral analysis for prediction of countershock success in a porcine model of ventricular fibrillation.
Resuscitation 2001;50(3):287-96.
2001: L D Schuler; Peter Walde; Pier Luigi Luisi; Wilfred F van Gunsteren
Molecular dynamics simulation of n-dodecyl phosphate aggregate structures.
European biophysics journal : EBJ 2001;30(5):330-43.
2001: Christine Peter; Xavier Daura; Wilfred F van Gunsteren
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.
Journal of biomolecular NMR 2001;20(4):297-310.
2001: J W Pitera; M Falta; Wilfred F van Gunsteren
Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.
Biophysical journal 2001;80(6):2546-55.
2001: Regula Walser; Philippe H Hünenberger; Wilfred F van Gunsteren
Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal.
Proteins 2001;43(4):509-19.
2001: Ronen Zangi; Helena Kovacs; Wilfred F van Gunsteren; J Johansson; Alan E Mark
Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C.
Proteins 2001;43(4):395-402.
2001: Roland Bürgi; J Pitera; Wilfred F van Gunsteren
Assessing the effect of conformational averaging on the measured values of observables.
Journal of biomolecular NMR 2001;19(4):305-20.
2001: H Schäfer; Xavier Daura; Alan E Mark; Wilfred F van Gunsteren
Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.
Proteins 2001;43(1):45-56.
2001: Xavier Daura; Karl Gademann; H Schäfer; Bernhard Jaun; Dieter Seebach; Wilfred F van Gunsteren
The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation.
Journal of the American Chemical Society 2001;123(10):2393-404.
2001: Regula Walser; Wilfred F van Gunsteren
Viscosity dependence of protein dynamics.
Proteins 2001;42(3):414-21.
2001: Roland Bürgi; Xavier Daura; A Mark; Massimo Bellanda; Stefano Mammi; Evaristo Peggion; Wilfred F van Gunsteren
Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations.
The journal of peptide research : official journal of the American Peptide Society 2001;57(2):107-18.
2001: Massimo Bellanda; Evaristo Peggion; Roland Bürgi; Wilfred F van Gunsteren; Stefano Mammi
Conformational study of an Aib-rich peptide in DMSO by NMR.
The journal of peptide research : official journal of the American Peptide Society 2001;57(2):97-106.
2000: C D Berweger; W Thiel; Wilfred F van Gunsteren
Molecular-dynamics simulation of the beta domain of metallothionein with a semi-empirical treatment of the metal core.
Proteins 2000;41(3):299-315.
2000: U Stocker; K Spiegel; Wilfred F van Gunsteren
On the similarity of properties in solution or in the crystalline state: a molecular dynamics study of hen lysozyme.
Journal of biomolecular NMR 2000;18(1):1-12.
2000: Xavier Daura; E Haaksma; Wilfred F van Gunsteren
Factor Xa: simulation studies with an eye to inhibitor design.
Journal of computer-aided molecular design 2000;14(6):507-29.
2000: S Voordijk; T Hansson; Donald Hilvert; Wilfred F van Gunsteren
Molecular dynamics simulations highlight mobile regions in proteins: A novel suggestion for converting a murine V(H) domain into a more tractable species.
Journal of molecular biology 2000;300(4):963-73.
2000: Regula Walser; Alan E Mark; Wilfred F van Gunsteren
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.
Biophysical journal 2000;78(6):2752-60.
2000: Alexandre Bonvin; Wilfred F van Gunsteren
beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat.
Journal of molecular biology 2000;296(1):255-68.
1999: Xavier Daura; I Antes; Wilfred F van Gunsteren; W Thiel; Alan E Mark
The effect of motional averaging on the calculation of NMR-derived structural properties.
Proteins 1999;36(4):542-55.
1999: C A Schiffer; Wilfred F van Gunsteren
Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study.
Proteins 1999;36(4):501-11.
1999: Lorna J Smith; Christopher M Dobson; Wilfred F van Gunsteren
Molecular dynamics simulations of human alpha-lactalbumin: changes to the structural and dynamical properties of the protein at low pH.
Proteins 1999;36(1):77-86.
1999: Lorna J Smith; Christopher M Dobson; Wilfred F van Gunsteren
Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin.
Journal of molecular biology 1999;286(5):1567-80.
1998: W R Scott; Alan E Mark; Wilfred F van Gunsteren
On using time-averaging restraints in molecular dynamics simulation.
Journal of biomolecular NMR 1998;12(4):501-8.
1998: Alexandre Bonvin; Maria Sunnerhagen; Gottfried Otting; Wilfred F van Gunsteren
Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator.
Journal of molecular biology 1998;282(4):859-73.
1998: Lorna J Smith; A E Mark; Christopher M Dobson; Wilfred F van Gunsteren
Molecular dynamics simulations of peptide fragments from hen lysozyme: insight into non-native protein conformations.
Journal of molecular biology 1998;280(4):703-19.
1997: A P Nanzer; A E Torda; C Bisang; C Weber; J A Robinson; Wilfred F van Gunsteren
Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations.
Journal of molecular biology 1997;267(4):1012-25.
1997: Helena Kovacs; Alan E Mark; Wilfred F van Gunsteren
Solvent structure at a hydrophobic protein surface.
Proteins 1997;27(3):395-404.
1997: P Ulrich; W Scott; Wilfred F van Gunsteren; Andrew E Torda
Protein structure prediction force fields: parametrization with quasi-newtonian dynamics.
Proteins 1997;27(3):367-84.
1996: J W Peng; C A Schiffer; P Xu; Wilfred F van Gunsteren; RR Ernst
Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide.
Journal of biomolecular NMR 1996;8(4):453-76.
1996: A P Nanzer; Thomas Huber; Andrew E Torda; Wilfred F van Gunsteren
Molecular dynamics simulation using weak-coupling NOE distance restraining.
Journal of biomolecular NMR 1996;8(3):285-91.
1996: C A Schiffer; Wilfred F van Gunsteren
Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study.
Proteins 1996;26(1):66-71.
1996: H Liu; F Müller-Plathe; Wilfred F van Gunsteren
A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease.
Journal of molecular biology 1996;261(3):454-69.
1995: C A Schiffer; V Dötsch; Kurt Wüthrich; Wilfred F van Gunsteren
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.
Biochemistry 1995;34(46):15057-67.
1995: A P Nanzer; Wilfred F van Gunsteren; Andrew E Torda
Parametrisation of time-averaged distance restraints in MD simulations.
Journal of biomolecular NMR 1995;6(3):313-20.
1995: P H Hünenberger; Alan E Mark; Wilfred F van Gunsteren
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations.
Journal of molecular biology 1995;252(4):492-503.
1995: J Fennen; Andrew E Torda; Wilfred F van Gunsteren
Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.
Journal of biomolecular NMR 1995;6(2):163-70.
1995: R M Brunne; K D Berndt; Peter Güntert; Kurt Wüthrich; Wilfred F van Gunsteren
Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations.
Proteins 1995;23(1):49-62.
1995: Lorna J Smith; Alan E Mark; Christopher M Dobson; Wilfred F van Gunsteren
Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes.
Biochemistry 1995;34(34):10918-31.
1995: Wilfred F van Gunsteren; P H Hünenberger; H Kovacs; Alan E Mark; C A Schiffer
Investigation of protein unfolding and stability by computer simulation.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1995;348(1323):49-59.
1995: H Kovacs; Alan E Mark; J Johansson; Wilfred F van Gunsteren
The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water.
Journal of molecular biology 1995;247(4):808-22.
1995: P H Hünenberger; Alan E Mark; Wilfred F van Gunsteren
Computational approaches to study protein unfolding: hen egg white lysozyme as a case study.
Proteins 1995;21(3):196-213.
1995: P E Smith; R C van Schaik; T Szyperski; Kurt Wüthrich; Wilfred F van Gunsteren
Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations.
Journal of molecular biology 1995;246(2):356-65.
1995: Alan E Mark; Y Xu; H Liu; Wilfred F van Gunsteren
Rapid non-empirical approaches for estimating relative binding free energies.
Acta biochimica Polonica 1995;42(4):525-35.
1994: A P Nanzer; F M Poulsen; Wilfred F van Gunsteren; Andrew E Torda
A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.
Biochemistry 1994;33(48):14503-11.
1994: Wilfred F van Gunsteren; P M King; Alan E Mark
Fundamentals of drug design from a biophysical viewpoint.
Quarterly reviews of biophysics 1994;27(4):435-81.
1994: Thomas Huber; Andrew E Torda; Wilfred F van Gunsteren
Local elevation: a method for improving the searching properties of molecular dynamics simulation.
Journal of computer-aided molecular design 1994;8(6):695-708.
1994: C A Schiffer; Robert Huber; Kurt Wüthrich; Wilfred F van Gunsteren
Simultaneous refinement of the structure of BPTI against NMR data measured in solution and X-ray diffraction data measured in single crystals.
Journal of molecular biology 1994;241(4):588-99.
1994: Alan E Mark; Wilfred F van Gunsteren
Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies.
Journal of molecular biology 1994;240(2):167-76.
1994: Nico A J van Nuland; I W Hangyi; R C van Schaik; Herman J C Berendsen; Wilfred F van Gunsteren; Ruud M Scheek; George T Robillard
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.
Journal of molecular biology 1994;237(5):544-59.
1994: X de la Cruz; Alan E Mark; J Tormo; Ignacio Fita; Wilfred F van Gunsteren
Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation.
Journal of molecular biology 1994;236(4):1186-95.
1994: P E Smith; Wilfred F van Gunsteren
Translational and rotational diffusion of proteins.
Journal of molecular biology 1994;236(2):629-36.
1994: Wilfred F van Gunsteren; F J Luque; D Timms; Andrew E Torda
Molecular mechanics in biology: from structure to function, taking account of solvation.
Annual review of biophysics and biomolecular structure 1994;23():847-63.
1994: Wilfred F van Gunsteren; R M Brunne; P Gros; R C van Schaik; C A Schiffer; Andrew E Torda
Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data.
Methods in enzymology 1994;239():619-54.
1993: R C van Schaik; Herman J C Berendsen; Andrew E Torda; Wilfred F van Gunsteren
A structure refinement method based on molecular dynamics in four spatial dimensions.
Journal of molecular biology 1993;234(3):751-62.
1993: R M Brunne; Edvards Liepinsh; Gottfried Otting; Kurt Wüthrich; Wilfred F van Gunsteren
Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations.
Journal of molecular biology 1993;231(4):1040-8.
1993: P R Gerber; Alan E Mark; Wilfred F van Gunsteren
An approximate but efficient method to calculate free energy trends by computer simulation: application to dihydrofolate reductase-inhibitor complexes.
Journal of computer-aided molecular design 1993;7(3):305-23.
1993: F Müller-Plathe; L Laaksonen; Wilfred F van Gunsteren
Cooperative effects in the transport of small molecules through an amorphous polymer matrix.
Journal of molecular graphics 1993;11(2):118-20, 125-6.
1993: A P Heiner; Herman J C Berendsen; Wilfred F van Gunsteren
Structure prediction of subtilisin BPN' mutants using molecular dynamics methods.
Protein engineering 1993;6(4):397-408.
1993: R M Brunne; Wilfred F van Gunsteren
Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm.
FEBS letters 1993;323(3):215-7.
1993: Y Y Shi; Alan E Mark; Cun Xin Wang; F Huang; H J Berendsen; Wilfred F van Gunsteren
Can the stability of protein mutants be predicted by free energy calculations?
Protein engineering 1993;6(3):289-95.
1993: Andrew E Torda; R M Brunne; Thomas Huber; H Kessler; Wilfred F van Gunsteren
Structure refinement using time-averaged J-coupling constant restraints.
Journal of biomolecular NMR 1993;3(1):55-66.
1992: A P Heiner; Herman J C Berendsen; Wilfred F van Gunsteren
MD simulation of subtilisin BPN' in a crystal environment.
Proteins 1992;14(4):451-64.
1992: Wilfred F van Gunsteren; Alan E Mark
Prediction of the activity and stability effects of site-directed mutagenesis on a protein core.
Journal of molecular biology 1992;227(2):389-95.
1992: Alan E Mark; Wilfred F van Gunsteren
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state.
Biochemistry 1992;31(34):7745-8.
1992: R C van Schaik; Wilfred F van Gunsteren; Herman J C Berendsen
Conformational search by potential energy annealing: algorithm and application to cyclosporin A.
Journal of computer-aided molecular design 1992;6(2):97-112.
1992: Wilfred F van Gunsteren; Alan E Mark
On the interpretation of biochemical data by molecular dynamics computer simulation.
European journal of biochemistry / FEBS 1992;204(3):947-61.
1991: Alan E Mark; H J Berendsen; Wilfred F van Gunsteren
Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study.
Biochemistry 1991;30(45):10866-72.
1991: Wilfred F van Gunsteren; P Gros; Andrew E Torda; H J Berendsen; R C van Schaik
On deriving spatial protein structure from NMR or X-ray diffraction data.
Ciba Foundation symposium 1991;161():150-9; discussion 159-66.
1991: J de Vlieg; Wilfred F van Gunsteren
Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data.
Methods in enzymology 1991;202():268-300.
1990: O Nilsson; Orlando Tapia; Wilfred F van Gunsteren
Structure and fluctuations of bacteriophage T4 glutaredoxin modelled by molecular dynamics.
Biochemical and biophysical research communications 1990;171(2):581-8.
1990: P Gros; Wilfred F van Gunsteren; Wim G J Hol
Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.
Science (New York, N.Y.) 1990;249(4973):1149-52.
1990: Andrew E Torda; Ruud M Scheek; Wilfred F van Gunsteren
Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.
Journal of molecular biology 1990;214(1):223-35.
1989: J de Vlieg; Herman J C Berendsen; Wilfred F van Gunsteren
An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution.
Proteins 1989;6(2):104-27.
1988: Andrew E Torda; Bridget C Mabbutt; Wilfred F van Gunsteren; Raymond S Norton
Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics.
FEBS letters 1988;239(2):266-70.
1988: Y Y Shi; R H Yun; Wilfred F van Gunsteren
Molecular dynamics simulation of despentapeptide insulin in a crystalline environment.
Journal of molecular biology 1988;200(3):571-7.
1988: Wilfred F van Gunsteren
The role of computer simulation techniques in protein engineering.
Protein engineering 1988;2(1):5-13.
1988: J de Vlieg; Ruud M Scheek; Wilfred F van Gunsteren; Herman J C Berendsen; R Kaptein; J Thomason
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.
Proteins 1988;3(4):209-18.
1987: Wilfred F van Gunsteren; Herman J C Berendsen
Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry.
Journal of computer-aided molecular design 1987;1(2):171-6.
1986: Johan Aqvist; P Sandblom; T A Jones; M E Newcomer; Wilfred F van Gunsteren; Orlando Tapia
Molecular dynamics simulations of the holo and apo forms of retinol binding protein. Structural and dynamical changes induced by retinol removal.
Journal of molecular biology 1986;192(3):593-603.
1986: P Sandblom; Johan Aqvist; T A Jones; M E Newcomer; Wilfred F van Gunsteren; Orlando Tapia
Structural changes in retinol binding protein induced by retinol removal. A molecular dynamics study.
Biochemical and biophysical research communications 1986;139(2):564-70.
1985: Johan Aqvist; Wilfred F van Gunsteren; M Leijonmarck; Orlando Tapia
A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein. Secondary structure motion in a 150 picosecond trajectory.
Journal of molecular biology 1985;183(3):461-77.