Wilfred F. van Gunsteren

Publication Activity (10 Years)

Years Active: 1987-2024
Publications (10 Years): 5

Top Topics

Molecular Dynamics

Gradient Vector Flow

Mathematical Models

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Maria Pechlaner, Wilfred F. van Gunsteren, Lorna J. Smith, Bartosz Stankiewicz, Lukas N. Wirz, Niels Hansen
Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach. J. Chem. Inf. Model. 64 (12) (2024)
Maria Pechlaner, Andreas P. Dorta, Zhixiong Lin, Victor H. Rusu, Wilfred F. van Gunsteren
A method to apply bond-angle constraints in molecular dynamics simulations. J. Comput. Chem. 42 (6) (2021)
Maria Pechlaner, Chris Oostenbrink, Wilfred F. van Gunsteren
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J. Comput. Chem. 42 (18) (2021)
Jozica Dolenc, Wilfred F. van Gunsteren, Andrea E. Prota, Michel O. Steinmetz, John H. Missimer
Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data. J. Chem. Inf. Model. 59 (5) (2019)
Oliwia M. Szklarczyk, Eirini Arvaniti, Wilfred F. van Gunsteren
Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. J. Comput. Chem. 36 (17) (2015)
Oliwia M. Szklarczyk, Stephan J. Bachmann, Wilfred F. van Gunsteren
A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons. J. Comput. Chem. 35 (10) (2014)
Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. PLoS Comput. Biol. 10 (12) (2014)
Zhixiong Lin, Wilfred F. van Gunsteren
Refinement of the application of the GROMOS 54A7 force field to β-peptides. J. Comput. Chem. 34 (32) (2013)
Zhixiong Lin, Wilfred F. van Gunsteren
Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation. J. Comput. Chem. 34 (22) (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. J. Comput. Chem. 34 (5) (2013)
Niels Hansen, Jozica Dolenc, Matthias Knecht, Sereina Riniker, 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. J. Comput. Chem. 33 (6) (2012)
Sereina Riniker, Luzi J. Barandun, François Diederich, Oliver Krämer, Andreas Steffen, Wilfred F. van Gunsteren
Free enthalpies of replacing water molecules in protein binding pockets. J. Comput. Aided Mol. Des. 26 (12) (2012)
Nathan Schmid, Clara D. Christ, Markus Christen, Andreas P. Eichenberger, Wilfred F. van Gunsteren
Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. Comput. Phys. Commun. 183 (4) (2012)
Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren, Philippe H. Hünenberger
-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol. J. Comput. Chem. 33 (24) (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. J. Comput. Chem. 33 (17) (2012)
Katharina Meier, Walter Thiel, Wilfred F. van Gunsteren
On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations. J. Comput. Chem. 33 (4) (2012)
Anna-Pitschna E. Kunz, Jane R. Allison, Daan P. Geerke, Bruno A. C. Horta, Philippe H. Hünenberger, Sereina Riniker, Nathan Schmid, Wilfred F. van Gunsteren
New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 33 (3) (2012)
Katharina Meier, Nathan Schmid, Wilfred F. van Gunsteren
Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages. J. Comput. Chem. 33 (26) (2012)
Zhixiong Lin, Wilfred F. van Gunsteren, Haiyan Liu
Conformational state-specific free energy differences by one-step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields. J. Comput. Chem. 32 (10) (2011)
Jozica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura, Wilfred F. van Gunsteren
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. J. Comput. Aided Mol. Des. 25 (8) (2011)
Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F. van Gunsteren
Calculation of binding free energies of inhibitors to plasmepsin II. J. Comput. Chem. 32 (9) (2011)
Nathan Schmid, Mathias Bötschi, Wilfred F. van Gunsteren
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software. J. Comput. Chem. 31 (8) (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. J. Comput. Chem. 31 (13) (2010)
David Poger, Wilfred F. van Gunsteren, Alan E. Mark
A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. 31 (6) (2010)
Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren
Basic ingredients of free energy calculations: A review. J. Comput. Chem. 31 (8) (2010)
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. J. Comput. Chem. 30 (11) (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. J. Comput. Chem. 30 (4) (2009)
Markus Christen, Wilfred F. van Gunsteren
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. J. Comput. Chem. 29 (2) (2008)
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. J. Comput. Chem. 27 (7) (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. J. Comput. Chem. 27 (13) (2006)
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. J. Comput. Chem. 26 (16) (2005)
Haibo Yu, Wilfred F. van Gunsteren
Accounting for polarization in molecular simulation. Comput. Phys. Commun. 172 (2) (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. J. Comput. Chem. 26 (7) (2005)
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. J. Comput. Chem. 25 (13) (2004)
Chris Oostenbrink, Wilfred F. van Gunsteren
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. J. Comput. Chem. 24 (14) (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. J. Comput. Chem. 24 (9) (2003)
Fred A. Hamprecht, Walter Thiel, Wilfred F. van Gunsteren
Chemical Library Subset Selection Algorithms: A Unified Derivation Using Spatial Statistics. J. Chem. Inf. Comput. Sci. 42 (2) (2002)
David B. Kony, Wolfgang Damm, Serge Stoll, Wilfred F. van Gunsteren
An improved OPLS-AA force field for carbohydrates. J. Comput. Chem. 23 (15) (2002)
Vincent Kräutler, Wilfred F. van Gunsteren, Philippe H. Hünenberger
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 22 (5) (2001)
Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. 22 (11) (2001)
Xavier Daura, Eric E. J. Haaksma, Wilfred F. van Gunsteren
Factor Xa: Simulation studies with an eye to inhibitor design. J. Comput. Aided Mol. Des. 14 (6) (2000)
Wolfgang Damm, Wilfred F. van Gunsteren
Reversible peptide folding: Dependence on molecular force field used. J. Comput. Chem. 21 (9) (2000)
Heiko Schäfer, Wilfred F. van Gunsteren, Alan E. Mark
Estimating relative free energies from a single ensemble: Hydration free energies. J. Comput. Chem. 20 (15) (1999)
Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren
Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. 19 (5) (1998)
Christian D. Berweger, Wilfred F. van Gunsteren, Florian Müller-Plathe
Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations. J. Comput. Chem. 18 (12) (1997)
H. Bekker, H. J. C. Berendesen, Wilfred F. van Gunsteren
Force and Cirial of Torsional-Angle-Dependent Potentials. J. Comput. Chem. 16 (5) (1995)
Andrew E. Torda, Wilfred F. van Gunsteren
Algorithms for Clustering Molecular Dynamics Confogurations. J. Comput. Chem. 15 (12) (1994)
Thomas Huber, Andrew E. Torda, Wilfred F. van Gunsteren
Local elevation: A method for improving the searching properties of molecular dynamics simulation. J. Comput. Aided Mol. Des. 8 (6) (1994)
Paul 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. J. Comput. Aided Mol. Des. 7 (3) (1993)
Anton Gunzinger, Urs A. Müller, Walter Scott, Bernhard Bäumle, Peter Kohler, Johann vonder Mühll, Florian Müller-Plathe, Wilfred F. van Gunsteren, Walter Guggenbühl
Achieving Super Computer Performance with a DSP Array Processor. SC (1992)
René C. van Schaik, Wilfred F. van Gunsteren, Herman J. C. Berendsen
Conformational search by potential energy annealing: Algorithm and application to cyclosporin A. J. Comput. Aided Mol. Des. 6 (2) (1992)
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. J. Comput. Aided Mol. Des. 1 (2) (1987)
J. Lautz, Horst Kessler, R. Kaptein, Wilfred F. van Gunsteren
Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data. J. Comput. Aided Mol. Des. 1 (3) (1987)