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Wilfred van Gunsteren

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Activities & Behaviors

Computer Simulation

Concepts & Ideas

Occupations

Thermodynamics

Phenomena

Physiology

Protein Folding

Chemicals & Drugs

Procedures

Genes & Molecular Sequences

Amino Acid Sequence

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Co-Publications
Name
25
Mark, Alan
20
Daura, Xavier
15
Oostenbrink, Chris
13
Hünenberger, Philippe
11
Torda, Andrew
11
Trzesniak, Daniel
9
Baron, Riccardo
9
Glättli, Alice
9
Christen, Markus
9
Berendsen, Herman
8
Jaun, Bernhard
7
Bakowies, Dirk
7
Geerke, Daan
7
Smith, Lorna
6
Yu, Haibo

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Publications

TOP 3
Gattin Z; Riniker S; Hore P J; Mok K H; van Gunsteren W F
Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations.
Kunz Anna-Pitschna E; van Gunsteren Wilfred F
Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D.
Wang Dongqi; Jaun Bernhard; van Gunsteren Wilfred F
Folding and unfolding of two mixed alpha/beta peptides.

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All Publications

2009: Gattin Z; Riniker S; Hore P J; Mok K H; van Gunsteren W F
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: Kunz Anna-Pitschna E; van Gunsteren Wilfred F
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: Wang Dongqi; Jaun Bernhard; van Gunsteren Wilfred F
Folding and unfolding of two mixed alpha/beta peptides.
Chembiochem : a European journal of chemical biology 2009;10(12):2032-41.
2009: Christ Clara D; Van Gunsteren Wilfred F
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: Lange Adam; Gattin Zrinka; Van Melckebeke Hélène; Wasmer Christian; Soragni Alice; van Gunsteren Wilfred F; Meier Beat H
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: Müller Christian L; Sbalzarini Ivo F; van Gunsteren Wilfred F; Zagrovic Bojan; Hünenberger Philippe H
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: Gattin Zrinka; van Gunsteren Wilfred F
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: Gattin Zrinka; Schwartz Julian; Mathad Raveendra I; Jaun Bernhard; van Gunsteren Wilfred F
Interpreting experimental data by using molecular simulation instead of model building.
Chemistry (Weinheim an der Bergstrasse, Germany) 2009;15(26):6389-98.
2009: Winger Moritz; Trzesniak Daniel; Baron Riccardo; van Gunsteren Wilfred F
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: Geerke Daan P; Luber Sandra; Marti Koni H; Van Gunsteren Wilfred F
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: Schmid Nathan; Bolliger Christine; Smith Lorna J; van Gunsteren Wilfred F
Disulfide bond shuffling in bovine alpha-lactalbumin: MD simulation confirms experiment.
Biochemistry 2008;47(46):12104-7.
2008: Dolenc Jozica; Baron Riccardo; Missimer John H; Steinmetz Michel O; van Gunsteren Wilfred F
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: Zagrovic Bojan; Gattin Zrinka; Lau Justin Kai-Chi; Huber Matthias; van Gunsteren Wilfred F
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: Christ Clara D; van Gunsteren Wilfred F
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: Gattin Zrinka; van Gunsteren Wilfred F
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: van Gunsteren Wilfred F; Dolenc Jozica; Mark Alan E
Molecular simulation as an aid to experimentalists.
Current opinion in structural biology 2008;18(2):149-53.
2008: Schwab Fabienne; van Gunsteren Wilfred F; Zagrovic Bojan
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: van Gunsteren Wilfred F; Dolenc Jozica
Biomolecular simulation: historical picture and future perspectives.
Biochemical Society transactions 2008;36(Pt 1):11-5.
2008: Steinmetz Michel O; Gattin Zrinka; Verel Rene; Ciani Barbara; Stromer Thusnelda; Green Janelle M; Tittmann Peter; Schulze-Briese Clemens; Gross Heinz; van Gunsteren Wilfred F; Meier Beat H; Serpell Louise C; Müller Shirley A; Kammerer Richard A
Atomic models of de novo designed cc beta-Met amyloid-like fibrils.
Journal of molecular biology 2008;376(3):898-912.
2008: Geerke Daan P; Thiel Stephan; Thiel Walter; van Gunsteren Wilfred F
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: Christen Markus; van Gunsteren Wilfred F
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: Boned Ricard; van Gunsteren Wilfred F; Daura Xavier
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: Christen Markus; Keller Bettina; van Gunsteren Wilfred F
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.
Journal of biomolecular NMR 2007;39(4):265-73.
2007: Cuendet Michel A; van Gunsteren Wilfred F
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: Missimer John H; Steinmetz Michel O; Baron Riccardo; Winkler Fritz K; Kammerer Richard A; Daura Xavier; van Gunsteren Wilfred F
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: Christen Markus; Christ Clara D; van Gunsteren Wilfred F
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: Kony David B; Damm Wolfgang; Stoll Serge; van Gunsteren Wilfred F; Hünenberger Philippe H
Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water.
Biophysical journal 2007;93(2):442-55.
2007: Kony David B; Hünenberger Philippe H; van Gunsteren Wilfred F
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: Geerke Daan P; van Gunsteren Wilfred F
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: Schmid Nathan; Zagrovic Bojan; van Gunsteren Wilfred F
Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA.
Biochemistry 2007;46(22):6500-12.
2007: Christ Clara D; van Gunsteren Wilfred F
Enveloping distribution sampling: a method to calculate free energy differences from a single simulation.
The Journal of chemical physics 2007;126(18):184110.
2007: Gattin Zrinka; Glättli Alice; Jaun Bernhard; van Gunsteren Wilfred F
Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibria.
Biopolymers 2007;85(4):318-32.
2007: Baron Riccardo; Trzesniak Daniel; de Vries Alex H; Elsener Andreas; Marrink Siewert J; van Gunsteren Wilfred F
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: Keller Bettina; Christen Markus; Oostenbrink Chris; van Gunsteren Wilfred F
On using oscillating time-dependent restraints in MD simulation.
Journal of biomolecular NMR 2007;37(1):1-14.
2007: Trzesniak Daniel; Kunz Anna-Pitschna E; van Gunsteren Wilfred F
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.
2006: Trzesniak Daniel; Jaun Bernhard; Mathad Raveendra I; van Gunsteren Wilfred F
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: Trzesniak Daniel; van Gunsteren Wilfred F
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: Smith Lorna J; Davies Robert J; van Gunsteren Wilfred F
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: Yu Haibo; Kohl Andreas; Binz H Kaspar; Plückthun Andreas; Grütter Markus G; van Gunsteren Wilfred F
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins.
Proteins 2006;65(2):285-95.
2006: Trzesniak Daniel; Lins Roberto D; van Gunsteren Wilfred F
Protein under pressure: molecular dynamics simulation of the arc repressor.
Proteins 2006;65(1):136-44.
2006: Yu Haibo; Geerke Daan P; Liu Haiyan; van Gunsteren Wilfred F
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.
Journal of computational chemistry 2006;27(13):1494-504.
2006: Baron Riccardo; de Vries Alex H; Hünenberger Philippe H; van Gunsteren Wilfred F
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: Dolenc Jozica; Baron Riccardo; Oostenbrink Chris; Koller Joze; van Gunsteren Wilfred F
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.
Biophysical journal 2006;91(4):1460-70.
2006: van der Vegt Nico F A; Lee Maeng-Eun; Trzesniak Daniel; van Gunsteren Wilfred F
Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions.
The journal of physical chemistry. B 2006;110(26):12852-5.
2006: van Gunsteren Wilfred F; Bakowies Dirk; Baron Riccardo; Chandrasekhar Indira; Christen Markus; Daura Xavier; Gee Peter; Geerke Daan P; Glättli Alice; Hünenberger Philippe H; Kastenholz Mika A; Oostenbrink Chris; Schenk Merijn; Trzesniak Daniel; van der Vegt Nico F A; Yu Haibo B
Biomolecular modeling: Goals, problems, perspectives.
Angewandte Chemie (International ed. in English) 2006;45(25):4064-92.
2006: Pereira Cristina S; Kony David; Baron Riccardo; Müller Martin; van Gunsteren Wilfred F; Hünenberger Philippe H
Conformational and dynamical properties of disaccharides in water: a molecular dynamics study.
Biophysical journal 2006;90(12):4337-44.
2006: Zhou Yu; Oostenbrink Chris; Jongejan Aldo; Van Gunsteren Wilfred F; Hagen Wilfred R; De Leeuw Simon W; Jongejan Jaap A
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: Christen Markus; van Gunsteren Wilfred F
Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.
The Journal of chemical physics 2006;124(15):154106.
2006: Christen Markus; Kunz Anna-Pitschna E; van Gunsteren Wilfred F
Sampling of rare events using hidden restraints.
The journal of physical chemistry. B 2006;110(16):8488-98.
2006: Baron Riccardo; de Vries Alex H; Hünenberger Philippe H; van Gunsteren Wilfred F
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: Gee Peter J; van Gunsteren Wilfred F
Terminal-group effects on the folding behavior of selected beta-peptides.
Proteins 2006;63(1):136-43.
2006: Zagrovic Bojan; van Gunsteren Wilfred F
Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
Proteins 2006;63(1):210-8.
2006: Geerke Daan P; van Gunsteren Wilfred F
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: Glättli Alice; Chandrasekhar Indira; van Gunsteren Wilfred F
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: Chandrasekhar Indira; van Gunsteren Wilfred F; Zandomeneghi Giorgia; Williamson Philip T F; Meier Beat H
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: Gee Peter J; van Gunsteren Wilfred F
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: Glättli Alice; Daura Xavier; Bindschädler Pascal; Jaun Bernhard; Mahajan Yogesh R; Mathad Raveendra I; Rueping Magnus; Seebach Dieter; van Gunsteren Wilfred F
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: Christen Markus; Hünenberger Philippe H; Bakowies Dirk; Baron Riccardo; Bürgi Roland; Geerke Daan P; Heinz Tim N; Kastenholz Mika A; Kräutler Vincent; Oostenbrink Chris; Peter Christine; Trzesniak Daniel; van Gunsteren Wilfred F
The GROMOS software for biomolecular simulation: GROMOS05.
Journal of computational chemistry 2005;26(16):1719-51.
2005: Trzesniak Daniel; Glättli Alice; Jaun Bernhard; van Gunsteren Wilfred F
Interpreting NMR data for beta-peptides using molecular dynamics simulations.
Journal of the American Chemical Society 2005;127(41):14320-9.
2005: Oostenbrink Chris; Juchli Daniel; van Gunsteren Wilfred F
Amine hydration: a united-atom force-field solution.
Chemphyschem : a European journal of chemical physics and physical chemistry 2005;6(9):1800-4.
2005: Missimer John H; Steinmetz Michel O; Jahnke Wolfgang; Winkler Fritz K; van Gunsteren Wilfred F; Daura Xavier
Molecular-dynamics simulations of C- and N-terminal peptide derivatives of GCN4-p1 in aqueous solution.
Chemistry & biodiversity 2005;2(8):1086-104.
2005: Zagrovic Bojan; Lipfert Jan; Sorin Eric J; Millett Ian S; van Gunsteren Wilfred F; Doniach Sebastian; Pande Vijay S
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: Oostenbrink Chris; van Gunsteren Wilfred F
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: de Vries Alex H; Chandrasekhar Indira; van Gunsteren Wilfred F; Hünenberger Philippe H
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: Oostenbrink Chris; Soares Thereza A; van der Vegt Nico F A; van Gunsteren Wilfred F
Validation of the 53A6 GROMOS force field.
European biophysics journal : EBJ 2005;34(4):273-84.
2005: Soares Thereza A; Hünenberger Philippe H; Kastenholz Mika A; Kräutler Vincent; Lenz Thomas; Lins Roberto D; Oostenbrink Chris; van Gunsteren Wilfred F
An improved nucleic acid parameter set for the GROMOS force field.
Journal of computational chemistry 2005;26(7):725-37.
2005: Oostenbrink Chris; van Gunsteren Wilfred F
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: Christen Markus; van Gunsteren Wilfred F
An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations.
The Journal of chemical physics 2005;122(14):144106.
2005: Kräutler Vincent; Aemissegger Andreas; Hünenberger Philippe H; Hilvert Donald; Hansson Tomas; van Gunsteren Wilfred F
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: van den Bosch Marieke; Swart Marcel; Snijders Jaap G; Berendsen Herman J C; Mark Alan E; Oostenbrink Chris; van Gunsteren Wilfred F; Canters Gerard W
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: Aemissegger Andreas; Kräutler Vincent; van Gunsteren Wilfred F; Hilvert Donald
A photoinducible beta-hairpin.
Journal of the American Chemical Society 2005;127(9):2929-36.
2005: Baron Riccardo; Bakowies Dirk; van Gunsteren Wilfred F
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: Smith Lorna J; Jones Rachel M; van Gunsteren Wilfred F
Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations.
Proteins 2005;58(2):439-49.
2005: Oostenbrink Chris; van Gunsteren Wilfred F
Methane clustering in explicit water: effect of urea on hydrophobic interactions.
Physical chemistry chemical physics : PCCP 2005;7(1):53-8.
2005: Hsu Shang-Te D; Peter Christine; van Gunsteren Wilfred F; Bonvin Alexandre M J J
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.
2005: Dolenc Jozica; Oostenbrink Chris; Koller Joze; van Gunsteren Wilfred F
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.
2004: Soares T A; Daura X; Oostenbrink C; Smith L J; van Gunsteren W F
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: Yu Haibo; van Gunsteren Wilfred F
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: van den Bosch M; Swart M; van Gunsteren W F; Canters Gerard W
Simulation of the substrate cavity dynamics of quercetinase.
Journal of molecular biology 2004;344(3):725-38.
2004: Glättli Alice; van Gunsteren Wilfred F
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: Oostenbrink Chris; Villa Alessandra; Mark Alan E; van Gunsteren Wilfred F
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: Santiveri Clara M; Jiménez M Angeles; Rico Manuel; Van Gunsteren Wilfred F; Daura Xavier
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: Baron Riccardo; Bakowies Dirk; van Gunsteren Wilfred F
Carbopeptoid folding: effects of stereochemistry, chain length, and solvent.
Angewandte Chemie (International ed. in English) 2004;43(31):4055-9.
2004: Yu Haibo; Amann Manfred; Hansson Tomas; Köhler Jutta; Wich Günter; van Gunsteren Wilfred F
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: Yu Haibo; Ramseier Maaike; Bürgi Roland; van Gunsteren Wilfred F
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: Calero Sofía; Lago Santiago; van Gunsteren Wilfred F; Daura Xavier
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: Peter Christine; Oostenbrink Chris; van Dorp Arthur; van Gunsteren Wilfred F
Estimating entropies from molecular dynamics simulations.
The Journal of chemical physics 2004;120(6):2652-61.
2004: Oostenbrink Chris; van Gunsteren Wilfred F
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation.
Proteins 2004;54(2):237-46.
2004: van der Vegt Nico F; Trzesniak Daniel; Kasumaj Besnik; van Gunsteren Wilfred F
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: Yu Haibo; Daura Xavier; van Gunsteren Wilfred F
Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding.
Proteins 2004;54(1):116-27.
2003: Peter Christine; Rueping Magnus; Wörner Hans Jakob; Jaun Bernhard; Seebach Dieter; van Gunsteren Wilfred F
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: Daura Xavier; Bakowies Dirk; Seebach Dieter; Fleischhauer Jörg; van Gunsteren Wilfred F; Krüger Peter
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: Oostenbrink Chris; van Gunsteren Wilfred F
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: Glättli Alice; Daura Xavier; Van Gunsteren Wilfred F
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: Chandrasekhar Indira; Kastenholz Mika; Lins Roberto D; Oostenbrink Chris; Schuler Lukas D; Tieleman D Peter; van Gunsteren Wilfred F
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: Antes Iris; Thiel Walter; van Gunsteren Wilfred F
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: Glättli Alice; Daura Xavier; Seebach Dieter; van Gunsteren Wilfred F
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: Kony D; Damm W; Stoll S; Van Gunsteren W F
An improved OPLS-AA force field for carbohydrates.
Journal of computational chemistry 2002;23(15):1416-29.
2002: Walser Regula; Hünenberger Philippe H; van Gunsteren Wilfred F
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: Smith Lorna J; Daura Xavier; van Gunsteren Wilfred F
Assessing equilibration and convergence in biomolecular simulations.
Proteins 2002;48(3):487-96.
2002: Feenstra K Anton; Peter Christine; Scheek Ruud M; van Gunsteren Wilfred F; Mark Alan E
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: Bakowies Dirk; Van Gunsteren Wilfred F
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: Bürgi Roland; Kollman Peter A; Van Gunsteren Wilfred F
Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.
Proteins 2002;47(4):469-80.
2002: Chandrasekhar Indira; van Gunsteren Wilfred F
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: Hamprecht Fred A; Thiel Walter; van Gunsteren Wilfred F
Chemical library subset selection algorithms: a unified derivation using spatial statistics.
Journal of chemical information and computer sciences 2002;42(2):414-28.
2002: Schäfer Heiko; Smith Lorna J; Mark Alan E; van Gunsteren Wilfred F
Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactalbumin.
Proteins 2002;46(2):215-24.
2002: Bakowies Dirk; van Gunsteren Wilfred F
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: Daura Xavier; Glättli Alice; Gee Peter; Peter Christine; van Gunsteren Wilfred F
Unfolded state of peptides.
Advances in protein chemistry 2002;62():341-60.
2001: Hamprecht F A; Achleitner U; Krismer A C; Lindner K H; Wenzel V; Strohmenger H U; Thiel W; van Gunsteren W F; Amann A
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: Schuler L D; Walde P; Luisi P L; van Gunsteren W F
Molecular dynamics simulation of n-dodecyl phosphate aggregate structures.
European biophysics journal : EBJ 2001;30(5):330-43.
2001: Peter C; Daura X; van Gunsteren W F
Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.
Journal of biomolecular NMR 2001;20(4):297-310.
2001: Pitera J W; Falta M; van Gunsteren W F
Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.
Biophysical journal 2001;80(6):2546-55.
2001: Walser R; Hünenberger P H; van Gunsteren W F
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: Zangi R; Kovacs H; van Gunsteren W F; Johansson J; Mark A E
Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C.
Proteins 2001;43(4):395-402.
2001: Bürgi R; Pitera J; van Gunsteren W F
Assessing the effect of conformational averaging on the measured values of observables.
Journal of biomolecular NMR 2001;19(4):305-20.
2001: Schäfer H; Daura X; Mark A E; van Gunsteren W F
Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.
Proteins 2001;43(1):45-56.
2001: Daura X; Gademann K; Schäfer H; Jaun B; Seebach D; van Gunsteren W F
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: Bürgi R; Daura X; Mark A; Bellanda M; Mammi S; Peggion E; van Gunsteren W
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: Bellanda M; Peggion E; Bürgi R; van Gunsteren W; Mammi S
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.
2001: Walser R; van Gunsteren W F
Viscosity dependence of protein dynamics.
Proteins 2001;42(3):414-21.
2000: Berweger C D; Thiel W; van Gunsteren W F
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: Stocker U; Spiegel K; van Gunsteren W F
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: Daura X; Haaksma E; van Gunsteren W F
Factor Xa: simulation studies with an eye to inhibitor design.
Journal of computer-aided molecular design 2000;14(6):507-29.
2000: Voordijk S; Hansson T; Hilvert D; van Gunsteren W F
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: Walser R; Mark A E; van Gunsteren W F
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: Bonvin A M; van Gunsteren W F
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: Daura X; Antes I; van Gunsteren W F; Thiel W; Mark A E
The effect of motional averaging on the calculation of NMR-derived structural properties.
Proteins 1999;36(4):542-55.
1999: Schiffer C A; van Gunsteren W F
Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study.
Proteins 1999;36(4):501-11.
1999: Smith L J; Dobson C M; van Gunsteren W F
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: Smith L J; Dobson C M; van Gunsteren W F
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: Bonvin A M; Sunnerhagen M; Otting G; van Gunsteren W F
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: Smith L J; Mark A E; Dobson C M; van Gunsteren W F
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: Nanzer A P; Torda A E; Bisang C; Weber C; Robinson J A; van Gunsteren W F
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: Kovacs H; Mark A E; van Gunsteren W F
Solvent structure at a hydrophobic protein surface.
Proteins 1997;27(3):395-404.
1997: Ulrich P; Scott W; van Gunsteren W F; Torda A E
Protein structure prediction force fields: parametrization with quasi-newtonian dynamics.
Proteins 1997;27(3):367-84.
1996: Schiffer C A; van Gunsteren W F
Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study.
Proteins 1996;26(1):66-71.
1996: Liu H; Müller-Plathe F; van Gunsteren W F
A combined quantum/classical molecular dynamics study of the catalytic mechanism of HIV protease.
Journal of molecular biology 1996;261(3):454-69.
1995: Schiffer C A; Dötsch V; Wüthrich K; van Gunsteren W F
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: Fennen J; Torda A E; van Gunsteren W F
Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.
Journal of biomolecular NMR 1995;6(2):163-70.
1995: Brunne R M; Berndt K D; Güntert P; Wüthrich K; van Gunsteren W F
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: Hünenberger P H; Mark A E; van Gunsteren W F
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations.
Journal of molecular biology 1995;252(4):492-503.
1995: Smith L J; Mark A E; Dobson C M; van Gunsteren W F
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: Van Gunsteren W F; Hünenberger P H; Kovacs H; Mark A E; Schiffer C A
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: Kovacs H; Mark A E; Johansson J; van Gunsteren W F
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: Hünenberger P H; Mark A E; van Gunsteren W F
Computational approaches to study protein unfolding: hen egg white lysozyme as a case study.
Proteins 1995;21(3):196-213.
1995: Smith P E; van Schaik R C; Szyperski T; Wüthrich K; van Gunsteren W F
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: Mark A E; Xu Y; Liu H; van Gunsteren W F
Rapid non-empirical approaches for estimating relative binding free energies.
Acta biochimica Polonica 1995;42(4):525-35.
1994: Nanzer A P; Poulsen F M; van Gunsteren W F; Torda A E
A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.
Biochemistry 1994;33(48):14503-11.
1994: van Gunsteren W F; King P M; Mark A E
Fundamentals of drug design from a biophysical viewpoint.
Quarterly reviews of biophysics 1994;27(4):435-81.
1994: Huber T; Torda A E; van Gunsteren W F
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: Schiffer C A; Huber R; Wüthrich K; van Gunsteren W F
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: Mark A E; van Gunsteren W F
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: van Nuland N A; Hangyi I W; van Schaik R C; Berendsen H J; van Gunsteren W F; Scheek R M; Robillard G T
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: de la Cruz X; Mark A E; Tormo J; Fita I; van Gunsteren W F
Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation.
Journal of molecular biology 1994;236(4):1186-95.
1994: Smith P E; van Gunsteren W F
Translational and rotational diffusion of proteins.
Journal of molecular biology 1994;236(2):629-36.
1994: van Gunsteren W F; Luque F J; Timms D; Torda A E
Molecular mechanics in biology: from structure to function, taking account of solvation.
Annual review of biophysics and biomolecular structure 1994;23():847-63.
1994: van Gunsteren W F; Brunne R M; Gros P; van Schaik R C; Schiffer C A; Torda A E
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: van Schaik R C; Berendsen H J; Torda A E; van Gunsteren W F
A structure refinement method based on molecular dynamics in four spatial dimensions.
Journal of molecular biology 1993;234(3):751-62.
1993: Gerber P R; Mark A E; van Gunsteren W F
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: Müller-Plathe F; Laaksonen L; van Gunsteren W F
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: Heiner A P; Berendsen H J; van Gunsteren W F
Structure prediction of subtilisin BPN' mutants using molecular dynamics methods.
Protein engineering 1993;6(4):397-408.
1993: Brunne R M; Liepinsh E; Otting G; Wüthrich K; van Gunsteren W F
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: Brunne R M; van Gunsteren W F
Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm.
FEBS letters 1993;323(3):215-7.
1993: Shi Y Y; Mark A E; Wang C X; Huang F; Berendsen H J; van Gunsteren W F
Can the stability of protein mutants be predicted by free energy calculations?
Protein engineering 1993;6(3):289-95.
1993: Torda A E; Brunne R M; Huber T; Kessler H; van Gunsteren W F
Structure refinement using time-averaged J-coupling constant restraints.
Journal of biomolecular NMR 1993;3(1):55-66.
1992: Heiner A P; Berendsen H J; van Gunsteren W F
MD simulation of subtilisin BPN' in a crystal environment.
Proteins 1992;14(4):451-64.
1992: Mark A E; van Gunsteren W F
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state.
Biochemistry 1992;31(34):7745-8.
1992: van Gunsteren W F; Mark A E
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: van Schaik R C; van Gunsteren W F; Berendsen H J
Conformational search by potential energy annealing: algorithm and application to cyclosporin A.
Journal of computer-aided molecular design 1992;6(2):97-112.
1992: van Gunsteren W F; Mark A E
On the interpretation of biochemical data by molecular dynamics computer simulation.
European journal of biochemistry / FEBS 1992;204(3):947-61.
1991: Mark A E; Berendsen H J; van Gunsteren W F
Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study.
Biochemistry 1991;30(45):10866-72.
1991: van Gunsteren W F; Gros P; Torda A E; Berendsen H J; van Schaik R C
On deriving spatial protein structure from NMR or X-ray diffraction data.
Ciba Foundation symposium 1991;161():150-9; discussion 159-66.
1991: de Vlieg J; van Gunsteren W F
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: Gros P; van Gunsteren W F; Hol W G
Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics.
Science (New York, N.Y.) 1990;249(4973):1149-52.
1990: Nilsson O; Tapia O; van Gunsteren W F
Structure and fluctuations of bacteriophage T4 glutaredoxin modelled by molecular dynamics.
Biochemical and biophysical research communications 1990;171(2):581-8.
1990: Torda A E; Scheek R M; van Gunsteren W F
Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.
Journal of molecular biology 1990;214(1):223-35.
1989: de Vlieg J; Berendsen H J; van Gunsteren W F
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: Torda A E; Mabbutt B C; van Gunsteren W F; Norton R S
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: Shi Y Y; Yun R H; van Gunsteren W F
Molecular dynamics simulation of despentapeptide insulin in a crystalline environment.
Journal of molecular biology 1988;200(3):571-7.
1988: van Gunsteren W F
The role of computer simulation techniques in protein engineering.
Protein engineering 1988;2(1):5-13.
1988: de Vlieg J; Scheek R M; van Gunsteren W F; Berendsen H J; Kaptein R; Thomason J
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: van Gunsteren W F; Berendsen H J
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: Aqvist J; Sandblom P; Jones T A; Newcomer M E; van Gunsteren W F; Tapia O
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: Sandblom P; Aqvist J; Jones T A; Newcomer M E; van Gunsteren W F; Tapia O
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: Aqvist J; van Gunsteren W F; Leijonmarck M; Tapia O
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.

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