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Wilfred F. van Gunsteren - Publications

Affiliations: 
Eidgenössische Technische Hochschule Zürich, Zürich, ZH, Switzerland 
Area:
molecular dynamics
Website:
http://www.igc.ethz.ch/people/wfvgn
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177 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Pechlaner M, van Gunsteren WF, Hansen N, Smith LJ. Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme. European Biophysics Journal : Ebj. 51: 265-282. PMID 35303138 DOI: 10.1007/s00249-022-01593-1  0.367
2021 Pechlaner M, Oostenbrink C, van Gunsteren WF. On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. Journal of Computational Chemistry. PMID 33951201 DOI: 10.1002/jcc.26541  0.581
2020 van Gunsteren WF, Daura X, Fuchs PFJ, Hansen N, Horta BAC, Hünenberger PH, Mark AE, Pechlaner M, Riniker S, Oostenbrink C. On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. PMID 33377305 DOI: 10.1002/cphc.202000968  0.724
2017 van Gunsteren WF, Daura X, Hansen N, Mark A, Oostenbrink C, Riniker S, Smith L. Validation of Molecular Simulation: An Overview of Issues. Angewandte Chemie (International Ed. in English). PMID 28682472 DOI: 10.1002/Anie.201702945  0.727
2017 Riniker S, van Gunsteren WF. Erratum: "Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system" [J. Chem. Phys. 137, 044120 (2012)]. The Journal of Chemical Physics. 146: 129901. PMID 28388170 DOI: 10.1063/1.4979127  0.59
2016 van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Deriving Structural Information from Experimentally Measured Data on Biomolecules. Angewandte Chemie (International Ed. in English). PMID 27862777 DOI: 10.1002/Anie.201601828  0.467
2015 Eichenberger AP, Huang W, Riniker S, van Gunsteren WF. Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase. Journal of Chemical Theory and Computation. 11: 2925-2937. PMID 26575730 DOI: 10.1021/Acs.Jctc.5B00295  0.599
2015 Eichenberger AP, van Gunsteren WF, Riniker S, von Ziegler L, Hansen N. The key to predicting the stability of protein mutants lies in an accurate description and proper configurational sampling of the folded and denatured states. Biochimica Et Biophysica Acta. 1850: 983-95. PMID 25239199 DOI: 10.1016/J.Bbagen.2014.09.014  0.559
2014 Huang W, Riniker S, van Gunsteren WF. Rapid Sampling of Folding Equilibria of β-Peptides in Methanol Using a Supramolecular Solvent Model. Journal of Chemical Theory and Computation. 10: 2213-23. PMID 26580745 DOI: 10.1021/Ct500048C  0.633
2014 Szklarczyk OM, Bachmann SJ, van Gunsteren WF. A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons. Journal of Computational Chemistry. 35: 789-801. PMID 26248885 DOI: 10.1002/jcc.23551  0.333
2014 Graf MM, Zhixiong L, Bren U, Haltrich D, van Gunsteren WF, Oostenbrink C. Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation. Plos Computational Biology. 10: e1003995. PMID 25500811 DOI: 10.1371/Journal.Pcbi.1003995  0.573
2014 Hansen N, Heller F, Schmid N, van Gunsteren WF. Time-averaged order parameter restraints in molecular dynamics simulations. Journal of Biomolecular Nmr. 60: 169-87. PMID 25312596 DOI: 10.1007/s10858-014-9866-7  0.308
2014 Lin Z, Oostenbrink C, van Gunsteren WF. On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters. European Biophysics Journal : Ebj. 43: 113-9. PMID 24504380 DOI: 10.1007/S00249-014-0943-3  0.546
2014 Huang W, Riniker S, Van Gunsteren WF. Rapid sampling of folding equilibria of β-peptides in methanol using a supramolecular solvent model Journal of Chemical Theory and Computation. 10: 2213-2223. DOI: 10.1021/ct500048c  0.528
2013 Lin Z, van Gunsteren WF. Combination of Enveloping Distribution Sampling (EDS) of a Soft-Core Reference-State Hamiltonian with One-Step Perturbation to Predict the Effect of Side Chain Substitution on the Relative Stability of Right- and Left-Helical Folds of β-Peptides. Journal of Chemical Theory and Computation. 9: 126-34. PMID 26589016 DOI: 10.1021/ct300929q  0.305
2013 Lin Z, Riniker S, van Gunsteren WF. Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water. Journal of Chemical Theory and Computation. 9: 1328-33. PMID 26587595 DOI: 10.1021/Ct3010497  0.644
2013 Eichenberger AP, van Gunsteren WF, Smith LJ. Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data. Journal of Biomolecular Nmr. 55: 339-53. PMID 23494634 DOI: 10.1007/s10858-013-9717-y  0.306
2013 Meier K, Choutko A, Dolenc J, Eichenberger AP, Riniker S, van Gunsteren WF. Multi-resolution simulation of biomolecular systems: a review of methodological issues. Angewandte Chemie (International Ed. in English). 52: 2820-34. PMID 23417997 DOI: 10.1002/Anie.201205408  0.597
2013 Lin Z, Riniker S, Van Gunsteren WF. Free enthalpy differences between α-, π-, and 3 10-helices of an atomic level fine-grained alanine deca-peptide solvated in supramolecular coarse-grained water Journal of Chemical Theory and Computation. 9: 1328-1333. DOI: 10.1021/ct3010497  0.552
2012 Riniker S, Barandun LJ, Diederich F, Krämer O, Steffen A, van Gunsteren WF. Free enthalpies of replacing water molecules in protein binding pockets. Journal of Computer-Aided Molecular Design. 26: 1293-309. PMID 23247390 DOI: 10.1007/S10822-012-9620-8  0.59
2012 Kleinjung J, Scott WR, Allison JR, van Gunsteren WF, Fraternali F. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 8: 2391-2403. PMID 23180979 DOI: 10.1021/ct200390j  0.321
2012 Lin Z, Timmerscheidt TA, van Gunsteren WF. 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. 137: 064108. PMID 22897256 DOI: 10.1063/1.4742751  0.309
2012 Riniker S, van Gunsteren WF. Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system. The Journal of Chemical Physics. 137: 044120. PMID 22852610 DOI: 10.1063/1.4739068  0.596
2012 Riniker S, Eichenberger AP, van Gunsteren WF. 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. 116: 8873-9. PMID 22816513 DOI: 10.1021/Jp304188Z  0.621
2012 Riniker S, Eichenberger AP, van Gunsteren WF. Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations. European Biophysics Journal : Ebj. 41: 647-61. PMID 22797564 DOI: 10.1007/S00249-012-0837-1  0.634
2012 Steiner D, van Gunsteren WF. An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation. European Biophysics Journal : Ebj. 41: 579-95. PMID 22706892 DOI: 10.1007/s00249-012-0824-6  0.306
2012 Riniker S, Allison JR, van Gunsteren WF. On developing coarse-grained models for biomolecular simulation: a review. Physical Chemistry Chemical Physics : Pccp. 14: 12423-30. PMID 22678152 DOI: 10.1039/C2Cp40934H  0.539
2012 Huang W, Eichenberger AP, van Gunsteren WF. Molecular dynamics simulation of thionated hen egg white lysozyme. Protein Science : a Publication of the Protein Society. 21: 1153-61. PMID 22653637 DOI: 10.1002/pro.2102  0.346
2012 Horta BA, Lin Z, Huang W, Riniker S, van Gunsteren WF, Hünenberger PH. 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. 33: 1907-17. PMID 22648867 DOI: 10.1002/Jcc.23021  0.587
2012 Steiner D, Oostenbrink C, van Gunsteren WF. Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9. Journal of Computational Chemistry. 33: 1467-77. PMID 22528559 DOI: 10.1002/Jcc.22972  0.561
2012 Riniker S, Horta BA, Thijssen B, Gupta S, van Gunsteren WF, Hünenberger PH. 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. 13: 1182-90. PMID 22383366 DOI: 10.1002/Cphc.201100949  0.57
2012 Allison JR, Riniker S, van Gunsteren WF. Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. The Journal of Chemical Physics. 136: 054505. PMID 22320749 DOI: 10.1063/1.3681140  0.612
2012 Hansen N, Dolenc J, Knecht M, Riniker S, van Gunsteren WF. 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. 33: 640-51. PMID 22228455 DOI: 10.1002/Jcc.22879  0.57
2012 Eichenberger AP, Smith LJ, van Gunsteren WF. Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation - possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold. The Febs Journal. 279: 299-315. PMID 22093234 DOI: 10.1111/j.1742-4658.2011.08424.x  0.325
2012 Kunz AP, Allison JR, Geerke DP, Horta BA, Hünenberger PH, Riniker S, Schmid N, van Gunsteren WF. New functionalities in the GROMOS biomolecular simulation software. Journal of Computational Chemistry. 33: 340-53. PMID 22076815 DOI: 10.1002/Jcc.21954  0.59
2011 Riniker S, Kunz AE, van Gunsteren WF. On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase. Journal of Chemical Theory and Computation. 7: 1469-1475. PMID 26610137 DOI: 10.1021/Ct100610V  0.604
2011 Lin Z, Liu H, Riniker S, van Gunsteren WF. On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and π-Helices. Journal of Chemical Theory and Computation. 7: 3884-97. PMID 26598335 DOI: 10.1021/Ct200623B  0.629
2011 Eichenberger AP, Allison JR, Dolenc J, Geerke DP, Horta BA, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang D, van Gunsteren WF. GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories. Journal of Chemical Theory and Computation. 7: 3379-90. PMID 26598168 DOI: 10.1021/Ct2003622  0.556
2011 Riniker S, Christ CD, Hansen HS, Hünenberger PH, Oostenbrink C, Steiner D, van Gunsteren WF. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software. The Journal of Physical Chemistry. B. 115: 13570-7. PMID 22039957 DOI: 10.1021/Jp204303A  0.724
2011 Riniker S, Christ CD, Hansen N, Mark AE, Nair PC, van Gunsteren WF. Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. The Journal of Chemical Physics. 135: 024105. PMID 21766923 DOI: 10.1063/1.3604534  0.612
2011 Dolenc J, Riniker S, Gaspari R, Daura X, van Gunsteren WF. Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. Journal of Computer-Aided Molecular Design. 25: 709-16. PMID 21735261 DOI: 10.1007/S10822-011-9453-X  0.548
2011 Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE, van Gunsteren WF. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal : Ebj. 40: 843-56. PMID 21533652 DOI: 10.1007/S00249-011-0700-9  0.568
2011 Steiner D, Oostenbrink C, Diederich F, Zürcher M, van Gunsteren WF. Calculation of binding free energies of inhibitors to plasmepsin II. Journal of Computational Chemistry. 32: 1801-12. PMID 21488062 DOI: 10.1002/Jcc.21761  0.573
2011 Allison JR, Boguslawski K, Fraternali F, van Gunsteren WF. A refined, efficient mean solvation force model that includes the interior volume contribution. The Journal of Physical Chemistry. B. 115: 4547-57. PMID 21434626 DOI: 10.1021/jp2017117  0.347
2011 Riniker S, van Gunsteren WF. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations. The Journal of Chemical Physics. 134: 084110. PMID 21361530 DOI: 10.1063/1.3553378  0.597
2011 Lin Z, Liu H, Riniker S, Van Gunsteren WF. On the use of enveloping distribution sampling (EDS) to compute free enthalpy differences between different conformational states of molecules: Application to 310-, α-, and π-helices Journal of Chemical Theory and Computation. 7: 3884-3897. DOI: 10.1021/ct200623b  0.552
2011 Eichenberger AP, Allison JR, Dolenc J, Geerke DP, Horta BAC, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang D, Van Gunsteren WF. GROMOS++ software for the analysis of biomolecular simulation trajectories Journal of Chemical Theory and Computation. 7: 3379-3390. DOI: 10.1021/ct2003622  0.525
2011 Riniker S, Kunz APE, Van Gunsteren WF. On the calculation of the dielectric permittivity and relaxation of molecular models in the liquid phase Journal of Chemical Theory and Computation. 7: 1469-1475. DOI: 10.1021/ct100610v  0.542
2010 Lin Z, Liu H, van Gunsteren WF. 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. 31: 2419-27. PMID 20652985 DOI: 10.1002/jcc.21534  0.334
2010 Riniker S, Daura X, Van Gunsteren WF. α-cyclodextrin host-guest binding: A computational study of the different driving forces Helvetica Chimica Acta. 93: 2318-2325. DOI: 10.1002/Hlca.201000251  0.622
2009 Allison JR, van Gunsteren WF. A method to explore protein side chain conformational variability using experimental data. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 10: 3213-28. PMID 19882615 DOI: 10.1002/cphc.200900400  0.326
2009 Gattin Z, Riniker S, Hore PJ, Mok KH, van Gunsteren WF. 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. 18: 2090-9. PMID 19693803 DOI: 10.1002/Pro.223  0.609
2009 Gattin Z, Schwartz J, Mathad RI, Jaun B, van Gunsteren WF. Interpreting experimental data by using molecular simulation instead of model building. Chemistry (Weinheim An Der Bergstrasse, Germany). 15: 6389-98. PMID 19462385 DOI: 10.1002/Chem.200802523  0.321
2008 Boned R, van Gunsteren WF, Daura X. Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations. Chemistry (Weinheim An Der Bergstrasse, Germany). 14: 5039-46. PMID 18399522 DOI: 10.1002/chem.200701380  0.314
2008 van Gunsteren WF, Dolenc J, Mark AE. Molecular simulation as an aid to experimentalists. Current Opinion in Structural Biology. 18: 149-53. PMID 18280138 DOI: 10.1016/j.sbi.2007.12.007  0.304
2008 Schwab F, van Gunsteren WF, Zagrovic B. Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase. Biochemistry. 47: 2945-51. PMID 18247576 DOI: 10.1021/Bi702067H  0.307
2008 Karplus M, Aminathan SSW, Ichiye T, Van Gunsteren WF. Local and Collective Motions in Protein Dynamics Ciba Foundation Symposium 93 - Mobility and Function in Proteins and Nucleic Acids. 271-290. DOI: 10.1002/9780470720752.ch15  0.345
2007 Christen M, Christ CD, van Gunsteren WF. Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 8: 1557-64. PMID 17577902 DOI: 10.1002/cphc.200700176  0.34
2007 Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 8: 452-61. PMID 17290360 DOI: 10.1002/cphc.200600658  0.535
2007 Kony DB, Damm W, Stoll S, van Gunsteren WF, Hünenberger PH. Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water. Biophysical Journal. 93: 442-55. PMID 17237195 DOI: 10.1529/biophysj.106.086116  0.314
2007 Keller B, Christen M, Oostenbrink C, van Gunsteren WF. On using oscillating time-dependent restraints in MD simulation Journal of Biomolecular Nmr. 37: 1-14. PMID 17180446 DOI: 10.1007/S10858-006-9081-2  0.57
2007 Winger M, Yu H, Redfield C, Van Gunsteren WF. Molecular dynamics simulation of human interleukin-4: Comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability Molecular Simulation. 33: 1143-1154. DOI: 10.1080/08927020701613623  0.497
2006 Yu H, Kohl A, Binz HK, Plückthun A, Grütter MG, van Gunsteren WF. Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins. Proteins. 65: 285-95. PMID 16948156 DOI: 10.1002/Prot.20991  0.448
2006 Yu H, Geerke DP, Liu H, van Gunsteren WF. Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. Journal of Computational Chemistry. 27: 1494-504. PMID 16838298 DOI: 10.1002/Jcc.20429  0.496
2006 van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NF, et al. Biomolecular modeling: Goals, problems, perspectives. Angewandte Chemie (International Ed. in English). 45: 4064-92. PMID 16761306 DOI: 10.1002/Anie.200502655  0.6
2006 Dolenc J, Baron R, Oostenbrink C, Koller J, Van Gunsteren WF. Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding Biophysical Journal. 91: 1460-1470. PMID 16731550 DOI: 10.1529/Biophysj.105.074617  0.514
2006 Pereira CS, Kony D, Baron R, Müller M, Van Gunsteren WF, Hünenberger PH. Conformational and dynamical properties of disaccharides in water: A molecular dynamics study Biophysical Journal. 90: 4337-4344. PMID 16581848 DOI: 10.1529/biophysj.106.081539  0.305
2006 Zhou Y, Oostenbrink C, Jongejan A, Van Gunsteren WF, Hagen WR, De Leeuw SW, Jongejan JA. 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. 27: 857-67. PMID 16541426 DOI: 10.1002/Jcc.20378  0.545
2006 Zagrovic B, van Gunsteren WF. Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us? Proteins. 63: 210-8. PMID 16425239 DOI: 10.1002/Prot.20872  0.338
2006 Christen M, van Gunsteren WF. An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations. The Journal of Chemical Physics. 122: 144106. PMID 15847515 DOI: 10.1063/1.1872792  0.326
2006 Oostenbrink C, Van Gunsteren WF. Calculating zeros: Non-equilibrium free energy calculations Chemical Physics. 323: 102-108. DOI: 10.1016/J.Chemphys.2005.08.054  0.573
2006 van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, et al. Biomolekulare Modellierung: Ziele, Probleme, Perspektiven Angewandte Chemie. 118: 4168-4198. DOI: 10.1002/Ange.200502655  0.42
2005 Oostenbrink C, van Gunsteren WF. Methane clustering in explicit water: effect of urea on hydrophobic interactions. Physical Chemistry Chemical Physics : Pccp. 7: 53-8. PMID 19785172 DOI: 10.1039/B413167C  0.461
2005 Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF. The GROMOS software for biomolecular simulation: GROMOS05. Journal of Computational Chemistry. 26: 1719-51. PMID 16211540 DOI: 10.1002/Jcc.20303  0.711
2005 Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Sciences of the United States of America. 102: 11698-703. PMID 16085707 DOI: 10.1073/Pnas.0409693102  0.314
2005 Oostenbrink C, Juchli D, van Gunsteren WF. Amine hydration: a united-atom force-field solution. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 6: 1800-4. PMID 16075431 DOI: 10.1002/Cphc.200400542  0.538
2005 Oostenbrink C, van Gunsteren WF. Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations. Chemistry (Weinheim An Der Bergstrasse, Germany). 11: 4340-8. PMID 15880545 DOI: 10.1002/Chem.200401120  0.548
2005 Oostenbrink C, Soares TA, van der Vegt NF, van Gunsteren WF. Validation of the 53A6 GROMOS force field. European Biophysics Journal : Ebj. 34: 273-84. PMID 15803330 DOI: 10.1007/S00249-004-0448-6  0.533
2005 Soares TA, Hünenberger PH, Kastenholz MA, Kräutler V, Lenz T, Lins RD, Oostenbrink C, van Gunsteren WF. An improved nucleic acid parameter set for the GROMOS force field. Journal of Computational Chemistry. 26: 725-37. PMID 15770662 DOI: 10.1002/Jcc.20193  0.552
2005 Oostenbrink C, van Gunsteren WF. Free energies of ligand binding for structurally diverse compounds. Proceedings of the National Academy of Sciences of the United States of America. 102: 6750-4. PMID 15767587 DOI: 10.1073/Pnas.0407404102  0.519
2005 van den Bosch M, Swart M, Snijders JG, Berendsen HJ, Mark AE, Oostenbrink C, van Gunsteren WF, Canters GW. Calculation of the redox potential of the protein azurin and some mutants. Chembiochem : a European Journal of Chemical Biology. 6: 738-46. PMID 15747387 DOI: 10.1002/Cbic.200400244  0.753
2005 Dolenc J, Oostenbrink C, Koller J, van Gunsteren WF. Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site. Nucleic Acids Research. 33: 725-33. PMID 15687382 DOI: 10.1093/Nar/Gki195  0.56
2005 Baron R, Bakowies D, van Gunsteren WF. Principles of carbopeptoid folding: a molecular dynamics simulation study. Journal of Peptide Science : An Official Publication of the European Peptide Society. 11: 74-84. PMID 15635631 DOI: 10.1002/PSC.597  0.318
2005 Smith LJ, Jones RM, van Gunsteren WF. Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations. Proteins. 58: 439-49. PMID 15558602 DOI: 10.1002/prot.20287  0.324
2005 Hsu ST, Peter C, van Gunsteren WF, Bonvin AM. Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation. Biophysical Journal. 88: 15-24. PMID 15489307 DOI: 10.1529/Biophysj.104.044933  0.683
2005 Zhou Y, Oostenbrink C, Van Gunsteren WF, Hagen WR, De Leeuw SW, Jongejan JA. Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations Molecular Physics. 103: 1961-1969. DOI: 10.1080/00268970500096889  0.495
2005 Yu H, van Gunsteren WF. Accounting for polarization in molecular simulation Computer Physics Communications. 172: 69-85. DOI: 10.1016/J.Cpc.2005.01.022  0.521
2004 Yu H, van Gunsteren WF. Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice. The Journal of Chemical Physics. 121: 9549-64. PMID 15538877 DOI: 10.1063/1.1805516  0.436
2004 van den Bosch M, Swart M, van Gunsteren WF, Canters GW. Simulation of the substrate cavity dynamics of quercetinase. Journal of Molecular Biology. 344: 725-38. PMID 15533441 DOI: 10.1016/J.Jmb.2004.09.056  0.521
2004 Peter C, Oostenbrink C, van Dorp A, van Gunsteren WF. Estimating entropies from molecular dynamics simulations. The Journal of Chemical Physics. 120: 2652-61. PMID 15268408 DOI: 10.1063/1.1636153  0.719
2004 Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF. 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. 25: 1656-1676. PMID 15264259 DOI: 10.1002/Jcc.20090  0.526
2004 Yu H, Amann M, Hansson T, Köhler J, Wich G, van Gunsteren WF. Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study. Carbohydrate Research. 339: 1697-709. PMID 15220079 DOI: 10.1016/J.Carres.2004.05.003  0.465
2004 Yu H, Ramseier M, Bürgi R, van Gunsteren WF. 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. 5: 633-41. PMID 15179715 DOI: 10.1002/Cphc.200301026  0.501
2004 Yu H, Daura X, van Gunsteren WF. Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding. Proteins. 54: 116-27. PMID 14705028 DOI: 10.1002/Prot.10502  0.483
2004 Oostenbrink C, van Gunsteren WF. Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation. Proteins. 54: 237-46. PMID 14696186 DOI: 10.1002/Prot.10558  0.559
2004 Chandrasekhar I, Oostenbrink C, van Gunsteren WF. Simulating the Physiological Phase of Hydrated DPPC Bilayers: The Ester Moiety Soft Materials. 2: 27-45. DOI: 10.1081/Smts-120030764  0.523
2004 Geerke DP, Oostenbrink C, van der Vegt NFA, van Gunsteren WF. An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water Mixtures The Journal of Physical Chemistry B. 108: 1436-1445. DOI: 10.1021/Jp035034I  0.567
2003 Peter C, Rueping M, Wörner HJ, Jaun B, Seebach D, van Gunsteren WF. Molecular dynamics simulations of small peptides: can one derive conformational preferences from ROESY spectra? Chemistry (Weinheim An Der Bergstrasse, Germany). 9: 5838-49. PMID 14673855 DOI: 10.1002/Chem.200305147  0.651
2003 Oostenbrink C, van Gunsteren WF. Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character. Journal of Computational Chemistry. 24: 1730-9. PMID 12964191 DOI: 10.1002/Jcc.10304  0.552
2003 Chandrasekhar I, Kastenholz M, Lins RD, Oostenbrink C, Schuler LD, Tieleman DP, van Gunsteren WF. A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field. European Biophysics Journal : Ebj. 32: 67-77. PMID 12632209 DOI: 10.1007/S00249-002-0269-4  0.527
2003 Peter C, van Gunsteren WF, Hünenberger PH. A fast-Fourier transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: Algorithm and application to ionic solvation and ion–ion interaction The Journal of Chemical Physics. 119: 12205-12223. DOI: 10.1063/1.1624054  0.602
2002 Daura X, Glättli A, Gee P, Peter C, van Gunsteren WF. Unfolded state of peptides. Advances in Protein Chemistry. 62: 341-60. PMID 12418109 DOI: 10.1016/S0065-3233(02)62013-3  0.602
2002 Feenstra KA, Peter C, Scheek RM, van Gunsteren WF, Mark AE. A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr. 23: 181-94. PMID 12238590 DOI: 10.1023/A:1019854626147  0.647
2002 Smith LJ, Daura X, van Gunsteren WF. Assessing equilibration and convergence in biomolecular simulations. Proteins. 48: 487-96. PMID 12112673 DOI: 10.1002/prot.10144  0.307
2002 Bakowies D, van Gunsteren WF. Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. Journal of Molecular Biology. 315: 713-36. PMID 11812142 DOI: 10.1006/JMBI.2001.5202  0.329
2002 Peter C, Daura X, van Gunsteren WF. Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. Journal of Biomolecular Nmr. 20: 297-310. PMID 11563554 DOI: 10.1023/A:1011241030461  0.645
2002 Peter C, van Gunsteren WF, Hünenberger PH. Solving the Poisson equation for solute–solvent systems using fast Fourier transforms The Journal of Chemical Physics. 116: 7434-7451. DOI: 10.1063/1.1465396  0.558
2001 van Gunsteren WF, Bürgi R, Peter C, Daura X. The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State. Angewandte Chemie (International Ed. in English). 40: 351-355. PMID 29712400 DOI: 10.1002/1521-3773(20010119)40:2<351::Aid-Anie351>3.0.Co;2-6  0.609
2001 Van Gunsteren WF, Bürgi R, Peter C, Daura X. Reply. Angewandte Chemie (International Ed. in English). 40: 4616-4618. PMID 12404365 DOI: 10.1002/1521-3773(20011217)40:24<4616::AID-ANIE4616>3.0.CO;2-B  0.485
2001 Schuler LD, Walde P, Luisi PL, van Gunsteren WF. Molecular dynamics simulation of n-dodecyl phosphate aggregate structures. European Biophysics Journal : Ebj. 30: 330-43. PMID 11592690 DOI: 10.1007/s002490100155  0.32
2001 Daura X, Gademann K, Schäfer H, Jaun B, Seebach D, van Gunsteren WF. 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. 123: 2393-404. PMID 11456889 DOI: 10.1021/Ja003689G  0.302
2001 Bürgi R, Pitera J, van Gunsteren WF. Assessing the effect of conformational averaging on the measured values of observables. Journal of Biomolecular Nmr. 19: 305-20. PMID 11370777 DOI: 10.1023/A:1011295422203  0.304
2001 van Gunsteren WF, Bürgi R, Peter C, Daura X. The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged. Angewandte Chemie (International Ed. in English). 40: 351-355. PMID 11180322 DOI: 10.1002/1521-3773(20010119)40:2<351::AID-ANIE351>3.0.CO;2-6  0.54
2001 Hamprecht FA, Peter C, Daura X, Thiel W, van Gunsteren WF. A strategy for analysis of (molecular) equilibrium simulations: Configuration space density estimation, clustering, and visualization The Journal of Chemical Physics. 114: 2079-2089. DOI: 10.1063/1.1330216  0.591
2001 van Gunsteren WF, Bürgi R, Peter C, Daura X. Der Schlüssel zum Verständnis des Proteinfaltungsproblems liegt in der richtigen Beschreibung des denaturierten Zustandes Angewandte Chemie. 113: 363-367. DOI: 10.1002/1521-3757(20010119)113:2<363::Aid-Ange363>3.0.Co;2-J  0.51
2000 Stocker U, van Gunsteren WF. Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data. Proteins. 40: 145-53. PMID 10813839 DOI: 10.1002/(SICI)1097-0134(20000701)40:1<145::AID-PROT160>3.0.CO;2-Y  0.321
2000 Bonvin AM, van Gunsteren WF. beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat. Journal of Molecular Biology. 296: 255-68. PMID 10656830 DOI: 10.1006/jmbi.1999.3446  0.556
2000 Schäfer H, Mark AE, Van Gunsteren WF. Absolute entropies from molecular dynamics simulation trajectories Journal of Chemical Physics. 113: 7809-7817. DOI: 10.1063/1.1309534  0.303
2000 Peter C, Daura X, van Gunsteren WF. Peptides of Aminoxy Acids:  A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions Journal of the American Chemical Society. 122: 7461-7466. DOI: 10.1021/Ja000873T  0.631
1999 Schiffer CA, van Gunsteren WF. Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study. Proteins. 36: 501-11. PMID 10450092 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<501::Aid-Prot14>3.0.Co;2-1  0.473
1999 Smith LJ, Dobson CM, van Gunsteren WF. Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin. Journal of Molecular Biology. 286: 1567-80. PMID 10064716 DOI: 10.1006/Jmbi.1999.2545  0.301
1998 Scott WR, Mark AE, van Gunsteren WF. On using time-averaging restraints in molecular dynamics simulation. Journal of Biomolecular Nmr. 12: 501-8. PMID 20012761 DOI: 10.1023/A:1008306732538  0.339
1998 Bonvin AM, Sunnerhagen M, Otting G, van Gunsteren WF. Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. Journal of Molecular Biology. 282: 859-73. PMID 9743632 DOI: 10.1006/jmbi.1998.2034  0.54
1998 van Gunsteren WF, Mark AE. Validation of molecular dynamics simulation The Journal of Chemical Physics. 108: 6109-6116. DOI: 10.1063/1.476021  0.3
1997 Daura X, van Gunsteren WF, Rigo D, Jaun B, Seebach D. Studying the Stability of a Helical β-Heptapeptide by Molecular Dynamics Simulations Chemistry - a European Journal. 3: 1410-1417. DOI: 10.1002/Chem.19970030907  0.309
1996 Peng JW, Schiffer CA, Xu P, van Gunsteren WF, Ernst RR. 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. 8: 453-76. PMID 20859779 DOI: 10.1007/Bf00228147  0.544
1996 Schiffer CA, van Gunsteren WF. Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: a molecular dynamics study. Proteins. 26: 66-71. PMID 8880930 DOI: 10.1002/(Sici)1097-0134(199609)26:1<66::Aid-Prot6>3.0.Co;2-E  0.522
1996 Fraternali F, Van Gunsteren WF. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution. Journal of Molecular Biology. 256: 939-48. PMID 8601844 DOI: 10.1006/jmbi.1996.0139  0.39
1996 Brunne RM, Berndt KD, Güntert P, Wüthrich K, van Gunsteren WF. Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations. Proteins. 23: 49-62. PMID 8539250 DOI: 10.1002/PROT.340230107  0.342
1996 Daura X, Hünenberger PH, Mark AE, Querol E, Avilés FX, Van Gunsteren WF. Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions Journal of the American Chemical Society. 118: 6285-6294. DOI: 10.1021/ja9537944  0.305
1995 Schiffer CA, Gros P, van Gunsteren WF. Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system. Acta Crystallographica. Section D, Biological Crystallography. 51: 85-92. PMID 15299339 DOI: 10.1107/S0907444994007158  0.447
1995 Van Gunsteren WF, Hünenberger PH, Kovacs H, Mark AE, Schiffer CA. Investigation of protein unfolding and stability by computer simulation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 348: 49-59. PMID 7770486 DOI: 10.1098/Rstb.1995.0045  0.524
1995 Huber T, Torda AE, van Gunsteren WF. Local elevation: a method for improving the searching properties of molecular dynamics simulation. Journal of Computer-Aided Molecular Design. 8: 695-708. PMID 7738605 DOI: 10.1007/BF00124016  0.329
1995 Smith LJ, Mark AE, Dobson CM, Van Gunsteren WF. Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes Biochemistry. 34: 10918-10931. PMID 7662673 DOI: 10.1021/Bi00034A026  0.323
1995 Schiffer CA, Dötsch V, Wüthrich K, van Gunsteren WF. 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. 34: 15057-67. PMID 7578118 DOI: 10.1021/Bi00046A011  0.562
1995 Smith PE, van Schaik RC, Szyperski T, Wüthrich K, van Gunsteren WF. 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. 246: 356-65. PMID 7532721 DOI: 10.1006/Jmbi.1994.0090  0.457
1995 Smith PE, van Gunsteren WF. Reaction field effects on the simulated properties of liquid water Molecular Simulation. 15: 233-245. DOI: 10.1080/08927029508022337  0.425
1995 Tironi IG, Sperb R, Smith PE, van Gunsteren WF. A generalized reaction field method for molecular dynamics simulations The Journal of Chemical Physics. 102: 5451-5459. DOI: 10.1063/1.469273  0.493
1995 Bisang C, Weber C, Inglis J, Schiffer CA, van Gunsteren WF, Jelesarov I, Bosshard HR, Robinson JA. Stabilization of Type-I .beta.-Turn Conformations in Peptides Containing the NPNA-Repeat Motif of the Plasmodium falciparum Circumsporozoite Protein by Substituting Proline for (S)-.alpha.-Methylproline Journal of the American Chemical Society. 117: 7904-7915. DOI: 10.1021/Ja00135A008  0.426
1995 van Gunsteren WF, Hünenberger PH, Mark AE, Smith PE, Tironi IG. Computer simulation of protein motion Computer Physics Communications. 91: 305-319. DOI: 10.1016/0010-4655(95)00055-K  0.474
1994 van Nuland NA, Hangyi IW, van Schaik RC, Berendsen HJ, van Gunsteren WF, Scheek RM, Robillard GT. 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. 237: 544-59. PMID 8158637 DOI: 10.1006/Jmbi.1994.1254  0.625
1994 Leenders R, van Gunsteren WF, Berendsen HJ, Visser AJ. Molecular dynamics simulations of oxidized and reduced Clostridium beijerinckii flavodoxin. Biophysical Journal. 66: 634-45. PMID 8011895 DOI: 10.1016/S0006-3495(94)80837-9  0.621
1994 van Gunsteren WF, Brunne RM, Gros P, van Schaik RC, Schiffer CA, Torda AE. Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. Methods in Enzymology. 239: 619-54. PMID 7530320 DOI: 10.1016/S0076-6879(94)39024-X  0.463
1994 Schiffer CA, Huber R, Wüthrich K, van Gunsteren WF. 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. 241: 588-99. PMID 7520085 DOI: 10.1006/Jmbi.1994.1533  0.439
1994 Smith PE, van Gunsteren WF. Translational and rotational diffusion of proteins. Journal of Molecular Biology. 236: 629-36. PMID 7508990 DOI: 10.1006/Jmbi.1994.1172  0.413
1994 Tironi IG, Van Gunsteren WF. A molecular dynamics simulation study of chloroform Molecular Physics. 83: 381-403. DOI: 10.1080/00268979400101331  0.305
1994 Smith PE, van Gunsteren WF. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K The Journal of Chemical Physics. 100: 3169-3174. DOI: 10.1063/1.466407  0.361
1994 Smith PE, van Gunsteren WF. When Are Free Energy Components Meaningful? The Journal of Physical Chemistry. 98: 13735-13740. DOI: 10.1021/J100102A046  0.34
1993 Shi YY, Mark AE, Wang CX, Huang F, Berendsen HJ, van Gunsteren WF. Can the stability of protein mutants be predicted by free energy calculations? Protein Engineering. 6: 289-95. PMID 8506263 DOI: 10.1093/protein/6.3.289  0.611
1993 Gerber PR, Mark AE, van Gunsteren WF. 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. 7: 305-323. PMID 8377027 DOI: 10.1007/BF00125505  0.323
1993 Heiner AP, Berendsen HJ, van Gunsteren WF. Structure prediction of subtilisin BPN' mutants using molecular dynamics methods. Protein Engineering. 6: 397-408. PMID 8332597 DOI: 10.1093/Protein/6.4.397  0.608
1993 van Schaik RC, Berendsen HJ, Torda AE, van Gunsteren WF. A structure refinement method based on molecular dynamics in four spatial dimensions. Journal of Molecular Biology. 234: 751-62. PMID 8254671 DOI: 10.1006/Jmbi.1993.1624  0.591
1993 Smith PE, van Gunsteren WF. The viscosity of SPC and SPC/E water at 277 and 300 K Chemical Physics Letters. 215: 315-318. DOI: 10.1016/0009-2614(93)85720-9  0.39
1992 van Schaik RC, van Gunsteren WF, Berendsen HJ. Conformational search by potential energy annealing: algorithm and application to cyclosporin A. Journal of Computer-Aided Molecular Design. 6: 97-112. PMID 1624960 DOI: 10.1007/Bf00129422  0.61
1992 Van Gunsteren WF, Mark AE. On the interpretation of biochemical data by molecular dynamics computer simulation European Journal of Biochemistry. 204: 947-961. PMID 1551395 DOI: 10.1111/J.1432-1033.1992.TB16716.X  0.332
1992 Heiner AP, Berendsen HJ, van Gunsteren WF. MD simulation of subtilisin BPN' in a crystal environment. Proteins. 14: 451-64. PMID 1438183 DOI: 10.1002/prot.340140406  0.633
1991 Mark AE, Berendsen HJ, van Gunsteren WF. Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study. Biochemistry. 30: 10866-72. PMID 1932009 DOI: 10.1021/BI00109A009  0.567
1991 Torda AE, van Gunsteren WF. The refinement of NMR structures by molecular dynamics simulation Computer Physics Communications. 62: 289-296. DOI: 10.1016/0010-4655(91)90101-P  0.305
1990 Lautz J, Kessler H, van Gunsteren WF, Weber HP, Wenger RM. On the dependence of molecular conformation on the type of solvent environment: a molecular dynamics study of cyclosporin A. Biopolymers. 29: 1669-87. PMID 2386812 DOI: 10.1002/Bip.360291214  0.336
1990 Torda AE, Scheek RM, van Gunsteren WF. Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. Journal of Molecular Biology. 214: 223-35. PMID 2370663 DOI: 10.1016/0022-2836(90)90157-H  0.314
1989 Makinen MW, Troyer JM, van der Werff H, Berendsen HJ, van Gunsteren WF. Dynamical structure of carboxypeptidase A. Journal of Molecular Biology. 207: 201-16. PMID 2738924 DOI: 10.1016/0022-2836(89)90451-8  0.613
1989 de Vlieg J, Berendsen HJ, van Gunsteren WF. An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution. Proteins. 6: 104-27. PMID 2622902 DOI: 10.1002/prot.340060203  0.62
1989 Scheek RM, van Gunsteren WF, Kaptein R. Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data. Methods in Enzymology. 177: 204-18. PMID 2607980 DOI: 10.1016/0076-6879(89)77012-9  0.327
1989 Torda AE, Scheek RM, van Gunsteren WF. Time-dependent distance restraints in molecular dynamics simulations Chemical Physics Letters. 157: 289-294. DOI: 10.1016/0009-2614(89)87249-5  0.309
1988 Pepermans H, Tourwé D, Van Binst G, Boelens R, Scheek RM, Van Gunsteren WF, Kaptein R. The combined use of NMR, distance geometry, and restrained molecular dynamics for the conformational study of a cyclic somatostatin analogue. Biopolymers. 27: 323-38. PMID 3359005 DOI: 10.1002/Bip.360270211  0.315
1988 Koehler JE, Saenger W, van Gunsteren WF. Conformational differences between alpha-cyclodextrin in aqueous solution and in crystalline form. A molecular dynamics study. Journal of Molecular Biology. 203: 241-50. PMID 3184189 DOI: 10.1016/0022-2836(88)90105-2  0.308
1988 de Vlieg J, Scheek RM, van Gunsteren WF, Berendsen HJ, 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. 3: 209-18. PMID 3047742 DOI: 10.1002/Prot.340030402  0.621
1987 van Gunsteren WF, Berendsen HJ. Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. Journal of Computer-Aided Molecular Design. 1: 171-6. PMID 3504214 DOI: 10.1007/BF01676960  0.62
1986 van Gunsteren W. Molecular dynamics simulations: techniques, experimental basis and determination of free energies Journal of Molecular Graphics. 4: 181. DOI: 10.1016/0263-7855(86)80028-5  0.313
1984 van Gunsteren WF, Berendsen HJ. Computer simulation as a tool for tracing the conformational differences between proteins in solution and in the crystalline state. Journal of Molecular Biology. 176: 559-64. PMID 6205158 DOI: 10.1016/0022-2836(84)90177-3  0.65
1983 Swaminathan S, Ichiye T, van Gunsteren W, Karplus M. Time dependence of atomic fluctuations in proteins: analysis of local and collective motions in bovine pancreatic trypsin inhibitor. Biochemistry. 21: 5230-41. PMID 7171552 DOI: 10.1021/Bi00264A019  0.34
1983 van Gunsteren WF, Berendsen HJ, Hermans J, Hol WG, Postma JP. Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data. Proceedings of the National Academy of Sciences of the United States of America. 80: 4315-9. PMID 6576339 DOI: 10.1073/Pnas.80.14.4315  0.627
1982 Van Gunsteren WF, Berendsen HJ. Molecular dynamics: perspective for complex systems. Biochemical Society Transactions. 10: 301-5. PMID 7141081 DOI: 10.1042/BST0100301  0.567
1982 van Gunsteren WF, Karplus M. Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. Biochemistry. 21: 2259-74. PMID 6178423 DOI: 10.1021/Bi00539A001  0.494
1982 Van Gunsteren WF, Karplus M. Effect of constraints on the dynamics of macromolecules Macromolecules. 15: 1528-1544. DOI: 10.1021/Ma00234A015  0.372
1980 Van Gunsteren WF, Karplus M. A method for constrained energy minimization of macromolecules Journal of Computational Chemistry. 1: 266-274. DOI: 10.1002/Jcc.540010308  0.346
1977 van Gunsteren W, Berendsen H. Algorithms for macromolecular dynamics and constraint dynamics Molecular Physics. 34: 1311-1327. DOI: 10.1080/00268977700102571  0.595
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