Wilfred F. van Gunsteren

57 papers A 1Journal 55

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Correction to "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. Maria Pechlaner, Wilfred F. van Gunsteren, Lorna J. Smith, Bartosz Stankiewicz, Lukas N. Wirz, Niels Hansen
2025	J	`jnl`	Use of Measured Residual Dipolar Couplings to Calculate Residual Dipolar Couplings for a Protein Structure: A Case Study Using Hen Egg-White Lysozyme. J. Chem. Inf. Model. Maria Pechlaner, Wilfred F. van Gunsteren, Niels Hansen, Lorna J. Smith
2024	J	`jnl`	Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. J. Chem. Inf. Model. Wilfred F. van Gunsteren, Chris Oostenbrink
2024	J	`jnl`	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. Maria Pechlaner, Wilfred F. van Gunsteren, Lorna J. Smith, Bartosz Stankiewicz, Lukas N. Wirz, Niels Hansen
2021	J	`jnl`	A method to apply bond-angle constraints in molecular dynamics simulations. J. Comput. Chem. Maria Pechlaner, Andreas P. Dorta, Zhixiong Lin, Victor H. Rusu, Wilfred F. van Gunsteren
2021	J	`jnl`	On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J. Comput. Chem. Maria Pechlaner, Chris Oostenbrink, Wilfred F. van Gunsteren
2019	J	`jnl`	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. Jozica Dolenc, Wilfred F. van Gunsteren, Andrea E. Prota, Michel O. Steinmetz, John H. Missimer
2015	J	`jnl`	Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. J. Comput. Chem. Oliwia M. Szklarczyk, Eirini Arvaniti, Wilfred F. van Gunsteren
2014	J	`jnl`	A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons. J. Comput. Chem. Oliwia M. Szklarczyk, Stephan J. Bachmann, Wilfred F. van Gunsteren
2014	J	`jnl`	Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. PLoS Comput. Biol. Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink
2013	J	`jnl`	Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation. J. Comput. Chem. Zhixiong Lin, Wilfred F. van Gunsteren
2013	J	`jnl`	On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment. J. Comput. Chem. Zhixiong Lin, Wilfred F. van Gunsteren
2013	J	`jnl`	Refinement of the application of the GROMOS 54A7 force field to β-peptides. J. Comput. Chem. Zhixiong Lin, Wilfred F. van Gunsteren
2012	J	`jnl`	Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. Comput. Phys. Commun. Nathan Schmid, Clara D. Christ, Markus Christen, Andreas P. Eichenberger, Wilfred F. van Gunsteren
2012	J	`jnl`	Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. J. Comput. Chem. Niels Hansen, Jozica Dolenc, Matthias Knecht, Sereina Riniker, Wilfred F. van Gunsteren
2012	J	`jnl`	Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. J. Comput. Chem. Denise Steiner, Chris Oostenbrink, Wilfred F. van Gunsteren
2012	J	`jnl`	Free enthalpies of replacing water molecules in protein binding pockets. J. Comput. Aided Mol. Des. Sereina Riniker, Luzi J. Barandun, François Diederich, Oliver Krämer, Andreas Steffen, Wilfred F. van Gunsteren
2012	J	`jnl`	Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages. J. Comput. Chem. Katharina Meier, Nathan Schmid, Wilfred F. van Gunsteren
2012	J	`jnl`	New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 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
2012	J	`jnl`	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. Katharina Meier, Walter Thiel, Wilfred F. van Gunsteren
2012	J	`jnl`	Reoptimized interaction parameters for the peptide-backbone model compound J. Comput. Chem. Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren, Philippe H. Hünenberger
2011	J	`jnl`	Calculation of binding free energies of inhibitors to plasmepsin II. J. Comput. Chem. Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F. van Gunsteren
2011	J	`jnl`	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. Zhixiong Lin, Wilfred F. van Gunsteren, Haiyan Liu
2011	J	`jnl`	Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. J. Comput. Aided Mol. Des. Jozica Dolenc, Sereina Riniker, Roberto Gaspari, Xavier Daura, Wilfred F. van Gunsteren
2010	J	`jnl`	A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software. J. Comput. Chem. Nathan Schmid, Mathias Bötschi, Wilfred F. van Gunsteren
2010	J	`jnl`	A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. David Poger, Wilfred F. van Gunsteren, Alan E. Mark
2010	J	`jnl`	Basic ingredients of free energy calculations: A review. J. Comput. Chem. Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren
2010	J	`jnl`	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. Zhixiong Lin, Haiyan Liu, Wilfred F. van Gunsteren
2009	J	`jnl`	Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation. J. Comput. Chem. Clara D. Christ, Wilfred F. van Gunsteren
2009	J	`jnl`	On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. J. Comput. Chem. Daan P. Geerke, Sandra Luber, Koni H. Marti, Wilfred F. van Gunsteren
2008	J	`jnl`	On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. J. Comput. Chem. Markus Christen, Wilfred F. van Gunsteren
2006	J	`jnl`	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. Yu Zhou, Chris Oostenbrink, Aldo Jongejan, Wilfred F. van Gunsteren, Wilfred R. Hagen, Simon W. De Leeuw, Jaap A. Jongejan
2006	J	`jnl`	Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. J. Comput. Chem. Haibo Yu, Daan P. Geerke, Haiyan Liu, Wilfred F. van Gunsteren
2005	J	`jnl`	Accounting for polarization in molecular simulation. Comput. Phys. Commun. Haibo Yu, Wilfred F. van Gunsteren
2005	J	`jnl`	An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren
2005	J	`jnl`	The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 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
2004	J	`jnl`	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. Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren
2003	J	`jnl`	A novel approach for designing simple point charge models for liquid water with three interaction sites. J. Comput. Chem. Alice Glättli, Xavier Daura, Wilfred F. van Gunsteren
2003	J	`jnl`	Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. J. Comput. Chem. Chris Oostenbrink, Wilfred F. van Gunsteren
2002	J	`jnl`	An improved OPLS-AA force field for carbohydrates. J. Comput. Chem. David B. Kony, Wolfgang Damm, Serge Stoll, Wilfred F. van Gunsteren
2002	J	`jnl`	Chemical Library Subset Selection Algorithms: A Unified Derivation Using Spatial Statistics. J. Chem. Inf. Comput. Sci. Fred A. Hamprecht, Walter Thiel, Wilfred F. van Gunsteren
2001	J	`jnl`	A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. Vincent Kräutler, Wilfred F. van Gunsteren, Philippe H. Hünenberger
2001	J	`jnl`	An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren
2000	J	`jnl`	Factor Xa: Simulation studies with an eye to inhibitor design. J. Comput. Aided Mol. Des. Xavier Daura, Eric E. J. Haaksma, Wilfred F. van Gunsteren
2000	J	`jnl`	Reversible peptide folding: Dependence on molecular force field used. J. Comput. Chem. Wolfgang Damm, Wilfred F. van Gunsteren
1999	—	`ch.`	Estimating Relative Free Energies from a Single Simulation of the Initial State. Computational Molecular Dynamics Alan E. Mark, Heiko Schäfer, Haiyan Liu, Wilfred F. van Gunsteren
1999	J	`jnl`	Estimating relative free energies from a single ensemble: Hydration free energies. J. Comput. Chem. Heiko Schäfer, Wilfred F. van Gunsteren, Alan E. Mark
1998	J	`jnl`	Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren
1997	J	`jnl`	Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations. J. Comput. Chem. Christian D. Berweger, Wilfred F. van Gunsteren, Florian Müller-Plathe
1995	J	`jnl`	Force and Cirial of Torsional-Angle-Dependent Potentials. J. Comput. Chem. Henk Bekker, H. J. C. Berendesen, Wilfred F. van Gunsteren
1994	J	`jnl`	Algorithms for Clustering Molecular Dynamics Confogurations. J. Comput. Chem. Andrew Ernest Torda, Wilfred F. van Gunsteren
1994	J	`jnl`	Local elevation: A method for improving the searching properties of molecular dynamics simulation. J. Comput. Aided Mol. Des. Thomas Huber, Andrew Ernest Torda, Wilfred F. van Gunsteren
1993	J	`jnl`	An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. J. Comput. Aided Mol. Des. Paul R. Gerber, Alan E. Mark, Wilfred F. van Gunsteren
1992	A	`conf`	Achieving Super Computer Performance with a DSP Array Processor. SC Anton Gunzinger, Urs A. Müller, Walter Scott, Bernhard Bäumle, Peter Kohler, Johann vonder Mühll, Florian Müller-Plathe, Wilfred F. van Gunsteren, Walter Guggenbühl
1992	J	`jnl`	Conformational search by potential energy annealing: Algorithm and application to cyclosporin A. J. Comput. Aided Mol. Des. René C. van Schaik, Wilfred F. van Gunsteren, Herman J. C. Berendsen
1987	J	`jnl`	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. J. Lautz, Horst Kessler, R. Kaptein, Wilfred F. van Gunsteren
1987	J	`jnl`	Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. J. Comput. Aided Mol. Des. Wilfred F. van Gunsteren, Herman J. C. Berendsen