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Wilfred F. van Gunsteren
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- affiliation: ETH Zurich, Switzerland
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2020 – today
- 2024
- [j53]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): 4781-4801 (2024) - [j52]Wilfred F. van Gunsteren, Chris Oostenbrink:
Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. J. Chem. Inf. Model. 64(16): 6281-6304 (2024) - 2021
- [j51]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): 418-434 (2021) - [j50]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): 1263-1282 (2021)
2010 – 2019
- 2019
- [j49]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): 2218-2230 (2019) - 2015
- [j48]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): 1311-1321 (2015) - 2014
- [j47]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): 789-801 (2014) - [j46]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) - 2013
- [j45]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): 387-393 (2013) - [j44]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): 1899-1906 (2013) - [j43]Zhixiong Lin, Wilfred F. van Gunsteren:
Refinement of the application of the GROMOS 54A7 force field to β-peptides. J. Comput. Chem. 34(32): 2796-2805 (2013) - 2012
- [j42]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): 890-903 (2012) - [j41]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): 1293-1309 (2012) - [j40]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): 340-353 (2012) - [j39]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): 363-378 (2012) - [j38]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): 640-651 (2012) - [j37]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): 1467-1477 (2012) - [j36]Bruno A. C. Horta, Zhixiong Lin, Wei Huang, 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. J. Comput. Chem. 33(24): 1907-1917 (2012) - [j35]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): 2108-2117 (2012) - 2011
- [j34]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): 709-716 (2011) - [j33]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): 1801-1812 (2011) - [j32]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): 2290-2297 (2011) - 2010
- [j31]David Poger, Wilfred F. van Gunsteren, Alan E. Mark:
A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. 31(6): 1117-1125 (2010) - [j30]Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren:
Basic ingredients of free energy calculations: A review. J. Comput. Chem. 31(8): 1569-1582 (2010) - [j29]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): 1636-1643 (2010) - [j28]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): 2419-2427 (2010)
2000 – 2009
- 2009
- [j27]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): 514-523 (2009) - [j26]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): 1664-1679 (2009) - 2008
- [j25]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): 157-166 (2008) - 2006
- [j24]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): 857-867 (2006) - [j23]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): 1494-1504 (2006) - 2005
- [j22]Haibo Yu, Wilfred F. van Gunsteren:
Accounting for polarization in molecular simulation. Comput. Phys. Commun. 172(2): 69-85 (2005) - [j21]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): 725-737 (2005) - [j20]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): 1719-1751 (2005) - 2004
- [j19]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): 1656-1676 (2004) - 2003
- [j18]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): 1087-1096 (2003) - [j17]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): 1730-1739 (2003) - 2002
- [j16]David B. Kony, Wolfgang Damm, Serge Stoll, Wilfred F. van Gunsteren:
An improved OPLS-AA force field for carbohydrates. J. Comput. Chem. 23(15): 1416-1429 (2002) - [j15]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): 414-428 (2002) - 2001
- [j14]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): 501-508 (2001) - [j13]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): 1205-1218 (2001) - 2000
- [j12]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): 507-529 (2000) - [j11]Wolfgang Damm, Wilfred F. van Gunsteren:
Reversible peptide folding: Dependence on molecular force field used. J. Comput. Chem. 21(9): 774-787 (2000)
1990 – 1999
- 1999
- [j10]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): 1604-1617 (1999) - [p1]Alan E. Mark, Heiko Schäfer, Haiyan Liu, Wilfred F. van Gunsteren:
Estimating Relative Free Energies from a Single Simulation of the Initial State. Computational Molecular Dynamics 1999: 149-162 - 1998
- [j9]Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren:
Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. 19(5): 535-547 (1998) - 1997
- [j8]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): 1484-1495 (1997) - 1995
- [j7]Henk Bekker, H. J. C. Berendesen, Wilfred F. van Gunsteren:
Force and Cirial of Torsional-Angle-Dependent Potentials. J. Comput. Chem. 16(5): 527-533 (1995) - 1994
- [j6]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): 695-708 (1994) - [j5]Andrew E. Torda, Wilfred F. van Gunsteren:
Algorithms for Clustering Molecular Dynamics Confogurations. J. Comput. Chem. 15(12): 1331-1340 (1994) - 1993
- [j4]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): 305-323 (1993) - 1992
- [j3]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): 97-112 (1992) - [c1]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: 543-550
1980 – 1989
- 1987
- [j2]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): 171-176 (1987) - [j1]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): 219-241 (1987)
Coauthor Index
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