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Wilfred F. van Gunsteren - Publications

Affiliations: 
ETH Zürich, Zürich, ZH, Switzerland 
Area:
molecular dynamics
Website:
http://www.igc.ethz.ch/people/wfvgn

343 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
2020 Pechlaner M, van Gunsteren WF. Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations. The Journal of Chemical Physics. 152: 024109. PMID 31941329 DOI: 10.1063/1.5124923  0.64
2019 Dolenc J, van Gunsteren WF, Prota AE, Steinmetz MO, Missimer JH. Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data. Journal of Chemical Information and Modeling. PMID 30855963 DOI: 10.1021/acs.jcim.9b00171  0.48
2019 van Gunsteren WF. The Roots of Bio‐Molecular Simulation: The Eight‐Week CECAM Workshop ‘Models for Protein Dynamics’ of 1976 Helvetica Chimica Acta. 102. DOI: 10.1002/hlca.201800239  0.32
2017 Smith LJ, van Gunsteren WF, Hansen N. Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4. The Journal of Physical Chemistry. B. PMID 28640620 DOI: 10.1021/acs.jpcb.7b03647  0.52
2017 Smith LJ, Athill R, van Gunsteren WF, Hansen N. Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 28503764 DOI: 10.1002/chem.201700896  0.52
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  1
2017 van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte Angewandte Chemie. 130: 894-915. DOI: 10.1002/Ange.201702945  0.48
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  1
2016 Smith LJ, Rought Whitta G, Dolenc J, Wang D, van Gunsteren WF. A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents. Bioorganic & Medicinal Chemistry. PMID 27543388 DOI: 10.1016/j.bmc.2016.08.001  0.48
2016 Dolenc J, Meier BH, Rusu VH, van Gunsteren WF. Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion. Physical Chemistry Chemical Physics : Pccp. PMID 26804445 DOI: 10.1039/c6cp00057f  0.48
2016 Rusu VH, Bachmann S, van Gunsteren WF. GROMOS polarisable model for acetone Molecular Physics. 1-10. DOI: 10.1080/00268976.2015.1126366  1
2016 van Gunsteren WF, Allison JR, Daura X, Dolenc J, Hansen N, Mark AE, Oostenbrink C, Rusu VH, Smith LJ. Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle Angewandte Chemie. 128: 16222-16244. DOI: 10.1002/ange.201601828  0.36
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  1
2015 Lin Z, van Gunsteren WF. Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide. Journal of Chemical Theory and Computation. 11: 1983-6. PMID 26574403 DOI: 10.1021/acs.jctc.5b00210  0.56
2015 Szklarczyk OM, Bieler NS, Hünenberger PH, van Gunsteren WF. Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 11: 5447-63. PMID 26574333 DOI: 10.1021/acs.jctc.5b00406  1
2015 Lin Z, van Gunsteren WF. On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations. The Journal of Chemical Physics. 143: 034110. PMID 26203017 DOI: 10.1063/1.4926937  1
2015 Szklarczyk OM, Arvaniti E, van Gunsteren WF. Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. Journal of Computational Chemistry. 36: 1311-21. PMID 26013466 DOI: 10.1002/jcc.23929  1
2015 Lin Z, van Gunsteren WF. A comparison of pathway-independent and pathway-dependent methods in the calculation of conformational free enthalpy differences. Protein Science : a Publication of the Protein Society. PMID 25975696 DOI: 10.1002/pro.2695  0.56
2015 Smith LJ, van Gunsteren WF, Hansen N. Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations. European Biophysics Journal : Ebj. 44: 235-47. PMID 25820531 DOI: 10.1007/s00249-015-1018-9  1
2015 Lin Z, Bachmann SJ, van Gunsteren WF. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2. The Journal of Chemical Physics. 142: 094117. PMID 25747071 DOI: 10.1063/1.4913955  1
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  1
2015 Huang W, van Gunsteren WF. Challenge of representing entropy at different levels of resolution in molecular simulation. The Journal of Physical Chemistry. B. 119: 753-63. PMID 25147102 DOI: 10.1021/jp505045m  1
2015 Bachmann SJ, Van Gunsteren WF. Structural and energetic effects of the use of polarisable water to solvate proteins Molecular Physics. 113: 2815-2828. DOI: 10.1080/00268976.2015.1042085  1
2015 Lin Z, Van Gunsteren WF. Effects of polarizable solvent models upon the relative stability of an α-helical and a β-hairpin structure of an alanine decapeptide Journal of Chemical Theory and Computation. 11: 1983-1986. DOI: 10.1021/acs.jctc.5b00210  1
2014 Hansen N, van Gunsteren WF. Practical Aspects of Free-Energy Calculations: A Review. Journal of Chemical Theory and Computation. 10: 2632-47. PMID 26586503 DOI: 10.1021/ct500161f  0.52
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  1
2014 Bachmann SJ, Lin Z, Stafforst T, van Gunsteren WF, Dolenc J. On the Sensitivity of Peptide Nucleic Acid Duplex Formation and Crystal Dissolution to a Variation of Force-Field Parameters. Journal of Chemical Theory and Computation. 10: 391-400. PMID 26579918 DOI: 10.1021/ct400652w  0.56
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  1
2014 Bachmann SJ, van Gunsteren WF. An improved simple polarisable water model for use in biomolecular simulation. The Journal of Chemical Physics. 141: 22D515. PMID 25494786 DOI: 10.1063/1.4897976  1
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  1
2014 Bachmann SJ, van Gunsteren WF. Polarizable model for DMSO and DMSO-water mixtures. The Journal of Physical Chemistry. B. 118: 10175-86. PMID 25094040 DOI: 10.1021/jp5035695  1
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  1
2014 Huang W, Lin Z, van Gunsteren WF. Use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields. The Journal of Physical Chemistry. B. 118: 6424-30. PMID 24410325 DOI: 10.1021/jp411005x  1
2014 Bachmann SJ, Van Gunsteren WF. On the compatibility of polarisable and non-polarisable models for liquid water Molecular Physics. 112: 2761-2780. DOI: 10.1080/00268976.2014.910317  1
2014 Hansen N, Van Gunsteren WF. Practical aspects of free-energy calculations: A review Journal of Chemical Theory and Computation. 10: 2632-2647. DOI: 10.1021/ct500161f  1
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  1
2014 Bachmann SJ, Lin Z, Stafforst T, Van Gunsteren WF, Dolenc J. On the sensitivity of peptide nucleic acid duplex formation and crystal dissolution to a variation of force-field parameters Journal of Chemical Theory and Computation. 10: 391-400. DOI: 10.1021/ct400652w  1
2014 Lin Z, Necula C, Van Gunsteren WF. Using enveloping distribution sampling to compute the folding free enthalpy of a β-peptide with a very unstable folded conformation in solution: The advantage of focused sampling using EDS Chemical Physics. 428: 156-163. DOI: 10.1016/j.chemphys.2013.11.016  1
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. DOI: 10.1002/jcc.23551  1
2014 Huang W, Hansen N, Van Gunsteren WF. On the use of a supramolecular coarse-grained model for the solvent in simulations of the folding equilibrium of an octa-β-peptide in MeOH and H2O Helvetica Chimica Acta. 97: 1591-1605. DOI: 10.1002/hlca.201400219  1
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  0.56
2013 Hansen N, Hünenberger PH, van Gunsteren WF. Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients. Journal of Chemical Theory and Computation. 9: 1334-46. PMID 26587596 DOI: 10.1021/ct300933y  0.56
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  1
2013 Lin Z, van Gunsteren WF. Refinement of the application of the GROMOS 54A7 force field to β-peptides. Journal of Computational Chemistry. 34: 2796-805. PMID 24122968 DOI: 10.1002/jcc.23459  1
2013 Lin Z, van Gunsteren WF. Enhanced conformational sampling using enveloping distribution sampling. The Journal of Chemical Physics. 139: 144105. PMID 24116601 DOI: 10.1063/1.4824391  1
2013 Pechlaner M, Sigel RK, van Gunsteren WF, Dolenc J. Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations. Biochemistry. 52: 7099-113. PMID 24001362 DOI: 10.1021/bi400784r  1
2013 Wang D, Böckmann A, Dolenc J, Meier BH, van Gunsteren WF. On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water. The Journal of Physical Chemistry. B. 117: 11433-47. PMID 23998392 DOI: 10.1021/jp400655v  1
2013 Smith LJ, Roby Y, Allison JR, van Gunsteren WF. Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data. Biochemistry. 52: 5029-38. PMID 23834513 DOI: 10.1021/bi4006573  1
2013 Hansen N, Allison JR, Hodel FH, van Gunsteren WF. Relative free enthalpies for point mutations in two proteins with highly similar sequences but different folds. Biochemistry. 52: 4962-70. PMID 23802564 DOI: 10.1021/bi400272q  1
2013 Lin Z, van Gunsteren WF. Influence of variation of a side chain on the folding equilibrium of a β-peptide: limitations of one-step perturbation. Journal of Computational Chemistry. 34: 1899-906. PMID 23712925 DOI: 10.1002/jcc.23331  1
2013 Wang D, Ámundadóttir ML, van Gunsteren WF, Hünenberger PH. Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers. European Biophysics Journal : Ebj. 42: 521-37. PMID 23660988 DOI: 10.1007/s00249-013-0901-5  1
2013 Choutko A, Eichenberger AP, van Gunsteren WF, Dolenc J. Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase. Protein Science : a Publication of the Protein Society. 22: 809-22. PMID 23595942 DOI: 10.1002/pro.2264  1
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  1
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  1
2013 Müller MM, Allison JR, Hongdilokkul N, Gaillon L, Kast P, van Gunsteren WF, Marlière P, Hilvert D. Directed evolution of a model primordial enzyme provides insights into the development of the genetic code. Plos Genetics. 9: e1003187. PMID 23300488 DOI: 10.1371/Journal.Pgen.1003187  1
2013 van Gunsteren WF. The seven sins in academic behavior in the natural sciences. Angewandte Chemie (International Ed. in English). 52: 118-22. PMID 23203439 DOI: 10.1002/anie.201204076  1
2013 Smith LJ, Gunsteren WF, Allison JR. Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12. Protein Science : a Publication of the Protein Society. 22: 56-64. PMID 23139016 DOI: 10.1002/pro.2184  1
2013 Lin Z, van Gunsteren WF. On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment. Journal of Computational Chemistry. 34: 387-93. PMID 23081811 DOI: 10.1002/jcc.23146  1
2013 Meier K, Van Gunsteren WF. On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain Molecular Simulation. 39: 472-486. DOI: 10.1080/08927022.2012.743659  1
2013 Bachmann SJ, Dolenc J, Van Gunsteren WF. On the use of one-step perturbation to investigate the dependence of different properties of liquid water on a variation of model parameters from a single simulation Molecular Physics. 111: 2334-2344. DOI: 10.1080/00268976.2013.815374  1
2013 Lin Z, Van Gunsteren WF. The effect of branched side chains on the relative stability of α- and π-helices: A combination of the enveloping distribution sampling and one-step perturbation methods Molecular Physics. 111: 2126-2130. DOI: 10.1080/00268976.2013.793828  1
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  1
2013 Hansen N, Hünenberger PH, Van Gunsteren WF. Efficient combination of environment change and alchemical perturbation within the enveloping distribution sampling (EDS) scheme: Twin-system EDS and application to the determination of octanol-water partition coefficients Journal of Chemical Theory and Computation. 9: 1334-1346. DOI: 10.1021/ct300933y  1
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: 126-134. DOI: 10.1021/ct300929q  1
2013 Choutko A, Van Gunsteren WF. Conformational preferences of a β-octapeptide as function of solvent and force-field parameters Helvetica Chimica Acta. 96: 189-200. DOI: 10.1002/hlca.201200173  1
2013 Meier K, Choutko A, Dolenc J, Eichenberger AP, Riniker S, van Gunsteren WF. Biomolekulare Simulationen mit mehreren Auflösungsniveaus: ein Überblick über methodische Aspekte Angewandte Chemie. 125: 2888-2904. DOI: 10.1002/Ange.201205408  0.36
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  1
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  1
2012 Missimer JH, Steinmetz MO, van Gunsteren WF, Dolenc J. Influence of 63Ser phosphorylation and dephosphorylation on the structure of the stathmin helical nucleation sequence: a molecular dynamics study. Biochemistry. 51: 8455-63. PMID 22978582 DOI: 10.1021/bi300885y  1
2012 Choutko A, van Gunsteren WF. Molecular dynamics simulation of the last step of a catalytic cycle: product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis. Protein Science : a Publication of the Protein Society. 21: 1672-81. PMID 22898919 DOI: 10.1002/pro.2143  1
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  1
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  1
2012 Hofer TS, van Gunsteren WF. Exploring the properties of small molecule protein binding via molecular simulations: the TRSH-p53 core domain complex. Molecular Biosystems. 8: 2891-900. PMID 22847335 DOI: 10.1039/c2mb25166c  1
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  1
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  1
2012 Wang D, van Gunsteren WF, Chai Z. Recent advances in computational actinoid chemistry. Chemical Society Reviews. 41: 5836-65. PMID 22777520 DOI: 10.1039/c2cs15354h  1
2012 Meier K, Schmid N, van Gunsteren WF. Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages. Journal of Computational Chemistry. 33: 2108-17. PMID 22736402 DOI: 10.1002/jcc.23047  1
2012 Steiner D, Allison JR, Eichenberger AP, van Gunsteren WF. On the calculation of ³Jαβ-coupling constants for side chains in proteins. Journal of Biomolecular Nmr. 53: 223-46. PMID 22714630 DOI: 10.1007/s10858-012-9634-5  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Meier K, Thiel W, van Gunsteren WF. On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations. Journal of Computational Chemistry. 33: 363-78. PMID 22180225 DOI: 10.1002/Jcc.21962  1
2012 Niggli DA, Ebert MO, Lin Z, Seebach D, van Gunsteren WF. Helical content of a β(3)-octapeptide in methanol: molecular dynamics simulations explain a seeming discrepancy between conclusions derived from CD and NMR data. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 586-93. PMID 22162155 DOI: 10.1002/Chem.201102667  1
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  1
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  1
2012 Van Gunsteren WF, Dolenc J. Thirty-five years of biomolecular simulation: Development of methodology, force fields and software Molecular Simulation. 38: 1271-1281. DOI: 10.1080/08927022.2012.701744  1
2012 Kunz APE, Lin Z, Van Gunsteren WF. Test of a method for sampling the internal degrees of freedom of a flexible solute molecule based on adiabatic decoupling and temperature or force scaling Molecular Physics. 110: 407-417. DOI: 10.1080/00268976.2011.650716  1
2012 Schmid N, Christ CD, Christen M, Eichenberger AP, Van Gunsteren WF. Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation Computer Physics Communications. 183: 890-903. DOI: 10.1016/j.cpc.2011.12.014  1
2012 van Gunsteren WF. Die sieben Todsünden akademischen Handelns in der naturwissenschaftlichen Forschung Angewandte Chemie. 125: 128-132. DOI: 10.1002/ange.201204076  0.4
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  1
2011 Huang W, Lin Z, van Gunsteren WF. Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding. Journal of Chemical Theory and Computation. 7: 1237-43. PMID 26610119 DOI: 10.1021/ct100747y  0.68
2011 Keller B, Hünenberger P, van Gunsteren WF. An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. Journal of Chemical Theory and Computation. 7: 1032-1044. PMID 26606352 DOI: 10.1021/ct200069c  0.36
2011 Horta BA, Fuchs PF, van Gunsteren WF, Hünenberger PH. New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters. Journal of Chemical Theory and Computation. 7: 1016-1031. PMID 26606351 DOI: 10.1021/ct1006407  0.56
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  1
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  1
2011 Allison JR, Bergeler M, Hansen N, van Gunsteren WF. Current computer modeling cannot explain why two highly similar sequences fold into different structures. Biochemistry. 50: 10965-73. PMID 22082195 DOI: 10.1021/bi2015663  1
2011 Choutko A, van Gunsteren WF, Hünenberger PH. Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 3214-23. PMID 22045646 DOI: 10.1002/cphc.201100541  1
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  1
2011 Lin Z, van Gunsteren WF. Exploring the effect of side-chain substitutions upon the secondary structure preferences of β-peptides. The Journal of Physical Chemistry. B. 115: 12984-92. PMID 21967665 DOI: 10.1021/jp2053508  1
2011 Kunz AP, van Gunsteren WF. A method for conformational sampling of loops in proteins based on adiabatic decoupling and temperature or force scaling. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 2609-14. PMID 21954004 DOI: 10.1002/cphc.201100305  1
2011 Kunz AP, Liu H, van Gunsteren WF. Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling. The Journal of Chemical Physics. 135: 104106. PMID 21932875 DOI: 10.1063/1.3629450  1
2011 Schmid N, Allison JR, Dolenc J, Eichenberger AP, Kunz AP, van Gunsteren WF. Biomolecular structure refinement using the GROMOS simulation software. Journal of Biomolecular Nmr. 51: 265-81. PMID 21858640 DOI: 10.1007/s10858-011-9534-0  1
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  1
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  1
2011 Kuzmanic A, Kruschel D, van Gunsteren WF, Pannu NS, Zagrovic B. Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures. Journal of Molecular Biology. 411: 286-97. PMID 21645520 DOI: 10.1016/J.Jmb.2011.05.033  1
2011 Lin Z, Van Gunsteren WF, Liu H. Conformational state-specific free energy differences by one-step perturbation: protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields. Journal of Computational Chemistry. 32: 2290-7. PMID 21541965 DOI: 10.1002/jcc.21818  1
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  1
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  1
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  1
2011 Kunz AP, van Gunsteren WF. Enhancing the configurational sampling of ions in aqueous solution using adiabatic decoupling with translational temperature scaling. The Journal of Physical Chemistry. B. 115: 2931-6. PMID 21384935 DOI: 10.1021/jp110778k  1
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  1
2011 Choutko A, Glättli A, Fernández C, Hilty C, Wüthrich K, van Gunsteren WF. Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle. European Biophysics Journal : Ebj. 40: 39-58. PMID 20922370 DOI: 10.1007/s00249-010-0626-7  0.52
2011 Hansen N, Kraus P, Samannshausen H, Timmerscheidt T, Van Gunsteren WF. An effective force field for molecular dynamics simulations of dimethyl sulfone Molecular Physics. 109: 2593-2605. DOI: 10.1080/00268976.2011.624128  1
2011 Kunz APE, Eichenberger AP, Van Gunsteren WF. A simple, efficient polarizable molecular model for liquid carbon tetrachloride Molecular Physics. 109: 365-372. DOI: 10.1080/00268976.2010.533208  1
2011 Lin Z, Schmid N, Van Gunsteren WF. The effect of using a polarizable solvent model upon the folding equilibrium of different β-peptides Molecular Physics. 109: 493-506. DOI: 10.1080/00268976.2010.532163  1
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  1
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  1
2011 Keller B, Hünenberger P, Van Gunsteren WF. An analysis of the validity of markov state models for emulating the dynamics of classical molecular systems and ensembles Journal of Chemical Theory and Computation. 7: 1032-1044. DOI: 10.1021/ct200069c  1
2011 Huang W, Lin Z, Van Gunsteren WF. Validation of the GROMOS 54A7 force field with respect to β-peptide folding Journal of Chemical Theory and Computation. 7: 1237-1243. DOI: 10.1021/ct100747y  1
2011 Horta BAC, Fuchs PFJ, Van Gunsteren WF, Hünenberger PH. New interaction parameters for oxygen compounds in the GROMOS force field: Improved pure-liquid and solvation properties for alcohols, ethers, aldehydes, ketones, carboxylic acids, and esters Journal of Chemical Theory and Computation. 7: 1016-1031. DOI: 10.1021/ct1006407  1
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  1
2010 Satoh H, Hansen HS, Manabe S, van Gunsteren WF, Hünenberger PH. Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex. Journal of Chemical Theory and Computation. 6: 1783-97. PMID 26615839 DOI: 10.1021/ct1001347  1
2010 Lin Z, van Gunsteren WF. Using one-step perturbation to predict the folding equilibrium of differently stereochemically substituted β-peptides. Physical Chemistry Chemical Physics : Pccp. 12: 15442-7. PMID 21038037 DOI: 10.1039/c0cp00833h  1
2010 Missimer JH, Dolenc J, Steinmetz MO, van Gunsteren WF. Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements. Protein Science : a Publication of the Protein Society. 19: 2462-74. PMID 20954244 DOI: 10.1002/pro.528  1
2010 Allison JR, Müller M, van Gunsteren WF. A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability. Protein Science : a Publication of the Protein Society. 19: 2186-95. PMID 20853427 DOI: 10.1002/pro.504  1
2010 Allison JR, Moll GP, van Gunsteren WF. Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation. Biochemistry. 49: 6916-27. PMID 20695529 DOI: 10.1021/bi100383m  1
2010 Dolenc J, Gerster S, van Gunsteren WF. Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA. The Journal of Physical Chemistry. B. 114: 11164-72. PMID 20690690 DOI: 10.1021/jp100483f  1
2010 Wang D, Merz T, van Gunsteren WF. The thermal isomerization of the GFP chromophore: A computational study. Physical Chemistry Chemical Physics : Pccp. 12: 11051-61. PMID 20668775 DOI: 10.1039/c0cp00181c  1
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  1
2010 Dolenc J, Missimer JH, Steinmetz MO, van Gunsteren WF. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1. Journal of Biomolecular Nmr. 47: 221-35. PMID 20524044 DOI: 10.1007/s10858-010-9425-9  1
2010 Lin Z, Kornfeld J, Mächler M, van Gunsteren WF. Prediction of folding equilibria of differently substituted peptides using one-step perturbation. Journal of the American Chemical Society. 132: 7276-8. PMID 20459089 DOI: 10.1021/ja100879k  1
2010 Keller B, Gattin Z, van Gunsteren WF. What stabilizes the 3(14)-helix in beta3-peptides? A conformational analysis using molecular simulation. Proteins. 78: 1677-90. PMID 20186978 DOI: 10.1002/prot.22685  1
2010 Keller B, Daura X, van Gunsteren WF. Comparing geometric and kinetic cluster algorithms for molecular simulation data. The Journal of Chemical Physics. 132: 074110. PMID 20170218 DOI: 10.1063/1.3301140  1
2010 Gattin Z, Zaugg J, van Gunsteren WF. Structure determination of a flexible cyclic peptide based on NMR and MD simulation 3J-coupling. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 11: 830-5. PMID 20162655 DOI: 10.1002/cphc.200900501  1
2010 Schmid N, Bötschi M, van Gunsteren WF. A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software. Journal of Computational Chemistry. 31: 1636-43. PMID 20127715 DOI: 10.1002/jcc.21447  1
2010 Meier K, van Gunsteren WF. Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics. The Journal of Physical Chemistry. A. 114: 1852-9. PMID 20055405 DOI: 10.1021/jp906218f  1
2010 Christ CD, Mark AE, van Gunsteren WF. Basic ingredients of free energy calculations: a review. Journal of Computational Chemistry. 31: 1569-82. PMID 20033914 DOI: 10.1002/jcc.21450  1
2010 Poger D, Van Gunsteren WF, Mark AE. A new force field for simulating phosphatidylcholine bilayers. Journal of Computational Chemistry. 31: 1117-25. PMID 19827145 DOI: 10.1002/jcc.21396  1
2010 Geerke DP, Van Gunsteren WF, Hunenberger PH. Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: Preferential affinity/exclusion effects and their relevance for bioprotection Molecular Simulation. 36: 708-728. DOI: 10.1080/08927021003752804  1
2010 Lin Z, Kunz AP, Van Gunsteren WF. A one-site polarizable model for liquid chloroform: COS/C Molecular Physics. 108: 1749-1757. DOI: 10.1080/00268976.2010.489527  1
2010 Van Gunsteren WF, Winger M. Reply to the 'Comment on "on using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models"' by S. J. Marrink, X. Periole, D. Peter Tieleman and Alex H. de Vries, Phys. Chem. Chem. Phys., 2010, 12, DOI: 10.1039/b915293h Physical Chemistry Chemical Physics. 12: 2257-2258. DOI: 10.1039/b922516c  1
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  1
2010 Wang D, Friedmann M, Gattin Z, Jaun B, Van Gunsteren WF. The propensity of α-aminoisobutyric acid (=2-methylalanine; Aib) to induce helical secondary structure in an α-heptapeptide: A computational study Helvetica Chimica Acta. 93: 1513-1531. DOI: 10.1002/Hlca.200900420  1
2009 Christ CD, van Gunsteren WF. Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS). Journal of Chemical Theory and Computation. 5: 276-86. PMID 26610104 DOI: 10.1021/ct800424v  1
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  1
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  1
2009 Kunz AP, van Gunsteren WF. Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D. The Journal of Physical Chemistry. A. 113: 11570-9. PMID 19663490 DOI: 10.1021/jp903164s  1
2009 Wang D, Jaun B, van Gunsteren WF. Folding and unfolding of two mixed alpha/beta peptides. Chembiochem : a European Journal of Chemical Biology. 10: 2032-41. PMID 19575368 DOI: 10.1002/Cbic.200900125  1
2009 Müller CL, Sbalzarini IF, van Gunsteren WF, Zagrovi? B, Hünenberger PH. In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. The Journal of Chemical Physics. 130: 214904. PMID 19508095 DOI: 10.1063/1.3140090  1
2009 Christ CD, Van Gunsteren WF. Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation. Journal of Computational Chemistry. 30: 1664-79. PMID 19504591 DOI: 10.1002/jcc.21325  1
2009 Lange A, Gattin Z, Van Melckebeke H, Wasmer C, Soragni A, van Gunsteren WF, Meier BH. 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. 10: 1657-65. PMID 19504509 DOI: 10.1002/Cbic.200900019  1
2009 Gattin Z, van Gunsteren WF. Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide. The Journal of Physical Chemistry. B. 113: 8695-703. PMID 19485309 DOI: 10.1021/jp811106e  1
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  1
2009 Winger M, Trzesniak D, Baron R, van Gunsteren WF. On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Physical Chemistry Chemical Physics : Pccp. 11: 1934-41. PMID 19280004 DOI: 10.1039/b818713d  1
2009 Geerke DP, Luber S, Marti KH, Van Gunsteren WF. On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. Journal of Computational Chemistry. 30: 514-23. PMID 18680218 DOI: 10.1002/jcc.21070  1
2009 Winger M, De Vries AH, Van Gunsteren WF. Force-field dependence of the conformational properties of ,-dimethoxypolyethylene glycol Molecular Physics. 107: 1313-1321. DOI: 10.1080/00268970902794826  1
2008 Schmid N, Bolliger C, Smith LJ, van Gunsteren WF. Disulfide bond shuffling in bovine alpha-lactalbumin: MD simulation confirms experiment. Biochemistry. 47: 12104-7. PMID 18942855 DOI: 10.1021/bi8013455  1
2008 Dolenc J, Baron R, Missimer JH, Steinmetz MO, van Gunsteren WF. Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study. Chembiochem : a European Journal of Chemical Biology. 9: 1749-56. PMID 18553323 DOI: 10.1002/cbic.200800096  1
2008 Christ CD, van Gunsteren WF. Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions. The Journal of Chemical Physics. 128: 174112. PMID 18465915 DOI: 10.1063/1.2913050  1
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  1
2008 Zagrovic B, Gattin Z, Lau JK, Huber M, van Gunsteren WF. Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment. European Biophysics Journal : Ebj. 37: 903-12. PMID 18368403 DOI: 10.1007/s00249-008-0307-y  1
2008 Gattin Z, van Gunsteren WF. A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pH. Chembiochem : a European Journal of Chemical Biology. 9: 923-33. PMID 18348116 DOI: 10.1002/cbic.200700434  1
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  1
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  1
2008 Geerke DP, Thiel S, Thiel W, van Gunsteren WF. QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians. Physical Chemistry Chemical Physics : Pccp. 10: 297-302. PMID 18213415 DOI: 10.1039/B713197F  1
2008 van Gunsteren WF, Dolenc J. Biomolecular simulation: historical picture and future perspectives. Biochemical Society Transactions. 36: 11-5. PMID 18208376 DOI: 10.1042/BST0360011  1
2008 Steinmetz MO, Gattin Z, Verel R, Ciani B, Stromer T, Green JM, Tittmann P, Schulze-Briese C, Gross H, van Gunsteren WF, Meier BH, Serpell LC, Müller SA, Kammerer RA. Atomic models of de novo designed cc beta-Met amyloid-like fibrils. Journal of Molecular Biology. 376: 898-912. PMID 18178219 DOI: 10.1016/J.Jmb.2007.11.100  1
2008 Christen M, van Gunsteren WF. On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. Journal of Computational Chemistry. 29: 157-66. PMID 17570138 DOI: 10.1002/jcc.20725  1
2008 Christen M, Kunz APE, Van Gunsteren WF. Sampling of rare events using hidden restraints (Journal of Physical Chemistry B (2006) 110 (8488-8498)) Journal of Physical Chemistry B. 112: 11446. DOI: 10.1021/jp806613d  1
2008 Winger M, Van Gunsteren WF. Use of molecular-dynamics simulation for optimizing protein stability: Consensus-designed ankyrin repeat proteins Helvetica Chimica Acta. 91: 1605-1613. DOI: 10.1002/hlca.200890175  1
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  1
2007 Geerke DP, Thiel S, Thiel W, van Gunsteren WF. Combined QM/MM Molecular Dynamics Study on a Condensed-Phase SN2 Reaction at Nitrogen:  The Effect of Explicitly Including Solvent Polarization. Journal of Chemical Theory and Computation. 3: 1499-509. PMID 26633221 DOI: 10.1021/ct7000123  1
2007 Zagrovic B, van Gunsteren WF. Computational Analysis of the Mechanism and Thermodynamics of Inhibition of Phosphodiesterase 5A by Synthetic Ligands. Journal of Chemical Theory and Computation. 3: 301-11. PMID 26627173 DOI: 10.1021/Ct600322D  1
2007 Cuendet MA, van Gunsteren WF. On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm. The Journal of Chemical Physics. 127: 184102. PMID 18020625 DOI: 10.1063/1.2779878  1
2007 Christen M, Keller B, van Gunsteren WF. Biomolecular structure refinement based on adaptive restraints using local-elevation simulation. Journal of Biomolecular Nmr. 39: 265-73. PMID 17929172 DOI: 10.1007/s10858-007-9194-2  0.36
2007 Missimer JH, Steinmetz MO, Baron R, Winkler FK, Kammerer RA, Daura X, van Gunsteren WF. Configurational entropy elucidates the role of salt-bridge networks in protein thermostability. Protein Science : a Publication of the Protein Society. 16: 1349-59. PMID 17586770 DOI: 10.1110/ps.062542907  1
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  1
2007 Kony DB, Hünenberger PH, van Gunsteren WF. 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. 16: 1101-18. PMID 17525462 DOI: 10.1110/ps.062323407  1
2007 Christ CD, van Gunsteren WF. Enveloping distribution sampling: a method to calculate free energy differences from a single simulation. The Journal of Chemical Physics. 126: 184110. PMID 17508795 DOI: 10.1063/1.2730508  1
2007 Geerke DP, van Gunsteren WF. 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. 111: 6425-36. PMID 17508737 DOI: 10.1021/jp0706477  1
2007 Schmid N, Zagrovic B, van Gunsteren WF. Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA. Biochemistry. 46: 6500-12. PMID 17497933 DOI: 10.1021/Bi6026133  1
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  1
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  1
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  1
2007 Gattin Z, Glättli A, Jaun B, Van Gunsteren WF. Simulation of β-depsipeptides: The effect of missing hydrogen-bond donors on their folding equilibria Biopolymers. 85: 318-332. PMID 17173308 DOI: 10.1002/Bip.20658  1
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  1
2007 Geerke DP, Van Gunsteren WF. The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures Molecular Physics. 105: 1861-1881. DOI: 10.1080/00268970701444631  1
2007 Trzesniak D, Van Der Vegt NFA, Van Gunsteren WF. Analysis of neo-pentane-urea pair potentials of mean force in aqueous urea Molecular Physics. 105: 33-39. DOI: 10.1080/00268970601126742  1
2007 Geerke DP, Van Gunsteren WF. On the calculation of atomic forces in classical simulation using the charge-on-spring method to explicitly treat electronic polarization Journal of Chemical Theory and Computation. 3: 2128-2137. DOI: 10.1021/ct700164k  1
2007 El-Barghouthi MI, Schenk M, Zughul MB, Badwan AA, Van Gunsteren WF. Comparison of estimates of free energy for binding of mono- and di-substituted benzenes with α-cyclodextrin obtained by single-step perturbation and thermodynamic integration Journal of Inclusion Phenomena and Macrocyclic Chemistry. 57: 375-377. DOI: 10.1007/s10847-006-9257-0  1
2007 Schmid N, Zagrovic B, Van Gunsteren WF. Folding-unfolding equilibrium of a methylidene-substituted β-peptide Helvetica Chimica Acta. 90: 1966-1979. DOI: 10.1002/Hlca.200790204  1
2007 Trzesniak D, Kunz APE, Van Gunsteren WF. A comparison of methods to compute the potential of mean force Chemphyschem. 8: 162-169. DOI: 10.1002/cphc.200600527  1
2007 Van Gunsteren WF, Gattin Z. Simulation of Folding Equilibria Foldamers: Structure, Properties, and Applications. 173-192. DOI: 10.1002/9783527611478.ch6  1
2007 Van Gunsteren WF, Geerke DP, Trzesniak D, Oostenbrink C, Van Der Vegt NFA. Analysis of the driving forces for biomolecular solvation and association Proceedings of the International School of Physics "Enrico Fermi". 165: 177-191.  1
2006 Trzesniak D, Van Gunsteren WF. Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: Pathway prediction and reconciliation of X-ray crystallographic and NMR solution data Protein Science. 15: 2544-2551. PMID 17075133 DOI: 10.1110/ps.062356406  1
2006 Smith LJ, Davies RJ, Van Gunsteren WF. Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: Comparisons of the wild-type protein, a b-type variant, and the apo state Proteins: Structure, Function and Genetics. 65: 702-711. PMID 16981201 DOI: 10.1002/prot.21141  1
2006 Trzesniak D, Jaun B, Mathad RI, Van Gunsteren WF. Simulation of an all-β3-icosapeptide containing the 20 proteinogenic side chains: Effect of temperature, pH, counterions, solvent, and force field on helix stability Biopolymers. 83: 636-645. PMID 16967513 DOI: 10.1002/bip.20601  1
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  1
2006 Trzesniak D, Lins RD, Van Gunsteren WF. Protein under pressure: Molecular dynamics simulation of the Arc Repressor Proteins: Structure, Function and Genetics. 65: 136-144. PMID 16917942 DOI: 10.1002/prot.21034  1
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  1
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  1
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  1
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  1
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  1
2006 Geerke DP, Van Gunsteren WF. Force field evaluation for biomolecular simulation: Fenthalpies of solvation of polar and apolar compounds in various solvents Chemphyschem. 7: 671-678. PMID 16514695 DOI: 10.1002/cphc.200500510  1
2006 Gee PJ, Van Gunsteren WF. Terminal-group effects on the folding behavior of selected beta-peptides Proteins: Structure, Function and Genetics. 63: 136-143. PMID 16435370 DOI: 10.1002/prot.20839  1
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  1
2006 Chandrasekhar I, van Gunsteren WF, Zandomeneghi G, Williamson PT, Meier BH. 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. 128: 159-70. PMID 16390143 DOI: 10.1021/Ja054785Q  1
2006 Glättli A, Chandrasekhar I, Van Gunsteren WF. A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer European Biophysics Journal. 35: 255-267. PMID 16322979 DOI: 10.1007/s00249-005-0033-7  1
2006 Gee PJ, Van Gunsteren WF. Acetonitrile revisited: A molecular dynamics study of the liquid phase Molecular Physics. 104: 477-483. DOI: 10.1080/00268970500473450  1
2006 Christen M, Van Gunsteren WF. Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems Journal of Chemical Physics. 124. DOI: 10.1063/1.2187488  1
2006 Van Der Vegt NFA, Lee ME, Trzesniak D, Van Gunsteren WF. Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions Journal of Physical Chemistry B. 110: 12852-12855. DOI: 10.1021/jp062426r  1
2006 Baron R, De Vries AH, Hünenberger PH, Van Gunsteren WF. Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations Journal of Physical Chemistry B. 110: 15602-15614. DOI: 10.1021/jp061627s  1
2006 Baron R, De Vries AH, Hünenberger PH, Van Gunsteren WF. Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates Journal of Physical Chemistry B. 110: 8464-8473. DOI: 10.1021/jp055888y  1
2006 Trzesniak D, van Gunsteren WF. Pathway dependence of the efficiency of calculating free energy and entropy of solute-solute association in water Chemical Physics. 330: 410-416. DOI: 10.1016/j.chemphys.2006.09.012  1
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  1
2006 Gee PJ, Van Gunsteren WF. Numerical simulation of the pressure denaturation of a helical β-peptide heptamer solvated in methanol Helvetica Chimica Acta. 89: 475-482. DOI: 10.1002/hlca.200690048  1
2006 Oostenbrink C, Van Lipzig MMH, Van Gunsteren WF. Applications of molecular dynamics simulations in drug design Comprehensive Medicinal Chemistry Ii. 4: 651-668.  1
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  1
2005 Missimer JH, Steinmetz MO, Jahnke W, Winkler FK, van Gunsteren WF, Daura X. Molecular-dynamics simulations of C- and N-terminal peptide derivatives of GCN4-p1 in aqueous solution. Chemistry & Biodiversity. 2: 1086-104. PMID 17193192 DOI: 10.1002/cbdv.200590078  1
2005 Glättli A, Daura X, Bindschädler P, Jaun B, Mahajan YR, Mathad RI, Rueping M, Seebach D, van Gunsteren WF. 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). 11: 7276-93. PMID 16247825 DOI: 10.1002/Chem.200401129  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  0.32
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  0.96
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  1
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  0.64
2004 Calero S, Lago S, van Gunsteren WF, Daura X. 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. 1: 505-19. PMID 17191865 DOI: 10.1002/cbdv.200490044  0.8
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  1
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  1
2004 Santiveri CM, Jiménez MA, Rico M, Van Gunsteren WF, Daura X. 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. 10: 546-65. PMID 15473263 DOI: 10.1002/psc.564  0.8
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  1
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  1
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  1
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  1
2004 van der Vegt NF, Trzesniak D, Kasumaj B, van Gunsteren WF. 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. 5: 144-7. PMID 14999859 DOI: 10.1002/cphc.200300918  0.48
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  1
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  1
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  0.48
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  0.4
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  1
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  1
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  1
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  0.4
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  0.8
2002 Glättli A, Daura X, Seebach D, van Gunsteren WF. Can one derive the conformational preference of a beta-peptide from its CD spectrum? Journal of the American Chemical Society. 124: 12972-8. PMID 12405823 DOI: 10.1021/Ja020758D  0.8
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  1
2002 Walser R, Hünenberger PH, Van Gunsteren WF. 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: Structure, Function and Genetics. 48: 327-340. PMID 12112700 DOI: 10.1002/prot.10143  1
2002 Bürgi R, Kollman PA, Van Gunsteren WF. Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. Proteins. 47: 469-80. PMID 12001225 DOI: 10.1002/Prot.10046  1
2002 Schäfer H, Smith LJ, Mark AE, Van Gunsteren WF. Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin Proteins: Structure, Function and Genetics. 46: 215-224. PMID 11807950 DOI: 10.1002/prot.1166  1
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  0.4
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  0.8
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  0.8
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  1
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  1
2001 Walser R, Hünenberger PH, Van Gunsteren WF. Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal Proteins: Structure, Function and Genetics. 43: 509-519. PMID 11340666 DOI: 10.1002/prot.1062  1
2001 Zangi R, Kovacs H, Van Gunsteren WF, Johansson J, Mark AE. Free energy barrier estimation of unfolding the α-helical surfactant-associated polypeptide c Proteins: Structure, Function and Genetics. 43: 395-402. PMID 11340656 DOI: 10.1002/prot.1052  1
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  0.8
2001 Schäfer H, Daura X, Mark AE, Van Gunsteren WF. Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior Proteins: Structure, Function and Genetics. 43: 45-56. PMID 11170213 DOI: 10.1002/1097-0134(20010401)43:1<45::AID-PROT1016>3.0.CO;2-N  1
2001 Walser R, Van Gunsteren WF. Viscosity dependence of protein dynamics Proteins: Structure, Function and Genetics. 42: 414-421. PMID 11151012 DOI: 10.1002/1097-0134(20010215)42:3<414::AID-PROT110>3.0.CO;2-4  1
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  0.36
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  0.48
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  0.96
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  1
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  0.4
2000 Bonvin AMJJ, Mark AE, Van Gunsteren WF. GROMOS96 benchmarks for molecular simulation Computer Physics Communications. 128: 550-557. DOI: 10.1016/S0010-4655(99)00540-8  1
1999 Daura X, Antes I, Van Gunsteren WF, Thiel W, Mark AE. The effect of motional averaging on the calculation of NMR-derived structural properties Proteins: Structure, Function and Genetics. 36: 542-555. PMID 10450095 DOI: 10.1002/(Sici)1097-0134(19990901)36:4<542::Aid-Prot17>3.0.Co;2-M  1
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  0.72
1999 Daura X, Van Gunsteren WF, Mark AE. Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations Proteins: Structure, Function and Genetics. 34: 269-280. PMID 10024015 DOI: 10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0.CO;2-3  1
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  0.56
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  0.96
1998 Smith LJ, Mark AE, Dobson CM, Van Gunsteren WF. Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformations Journal of Molecular Biology. 280: 703-719. PMID 9677298 DOI: 10.1006/Jmbi.1998.1892  1
1998 Daura X, Jaun B, Seebach D, van Gunsteren WF, Mark AE. Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology. 280: 925-32. PMID 9671560 DOI: 10.1006/Jmbi.1998.1885  1
1997 Kovacs H, Mark AE, Van Gunsteren WF. Solvent structure at a hydrophobic protein surface Proteins: Structure, Function and Genetics. 27: 395-404. PMID 9094741 DOI: 10.1002/(SICI)1097-0134(199703)27:3<395::AID-PROT7>3.0.CO;2-C  1
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  1
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  0.72
1996 Luty BA, van Gunsteren WF. Calculating Electrostatic Interactions Using the Particle−Particle Particle−Mesh Method with Nonperiodic Long-Range Interactions The Journal of Physical Chemistry. 100: 2581-2587. DOI: 10.1021/jp9518623  0.4
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  1
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  0.72
1995 Hunenberger PH, Mark AE, Van Gunsteren WF. Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study Proteins: Structure, Function and Genetics. 21: 196-213. PMID 7784424 DOI: 10.1002/prot.340210303  1
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  1
1995 Kovacs H, Mark AE, Johansson J, van Gunsteren WF. 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. 247: 808-822. PMID 7723032 DOI: 10.1016/S0022-2836(05)80156-1  1
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  1
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  1
1995 Hunenberger PH, Mark AE, Van Gunsteren WF. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations Journal of Molecular Biology. 252: 492-503. PMID 7563068 DOI: 10.1006/jmbi.1995.0514  1
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  1
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  1
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  0.48
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  1
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  1
1994 de la Cruz X, Mark AE, Tormo J, Fita I, van Gunsteren WF. Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation Journal of Molecular Biology. 236: 1186-1195. PMID 8120895 DOI: 10.1016/0022-2836(94)90020-5  1
1994 Mark AE, Van Gunsteren WF. Decomposition of the free energy of a system in terms of specific interactions: Implications for theoretical and experimental studies Journal of Molecular Biology. 240: 167-176. PMID 8028000 DOI: 10.1006/JMBI.1994.1430  1
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  0.72
1994 Van Gunsteren WF, King PM, Mark AE. Fundamentals of drug design from a biophysical viewpoint Quarterly Reviews of Biophysics. 27: 435-481. PMID 7784540 DOI: 10.1017/S0033583500003103  1
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  0.72
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  0.72
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  1
1994 Smith PE, Gunsteren WFv. Predictions of free energy differences from a single simulation of the initial state The Journal of Chemical Physics. 100: 577-585. DOI: 10.1063/1.466975  0.76
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  0.64
1994 Smith PE, van Gunsteren WF. When Are Free Energy Components Meaningful? The Journal of Physical Chemistry. 98: 13735-13740. DOI: 10.1021/J100102A046  0.68
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  1
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  0.72
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  0.72
1993 El Tayar N, Mark AE, Vallat P, Brunne RM, Testa B, Van Gunsteren WF. Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A: Evidence from partition coefficients and molecular dynamics simulations Journal of Medicinal Chemistry. 36: 3757-3764. PMID 8254605 DOI: 10.1021/jm00076a002  1
1993 Gros P, Van Gunsteren WF. Crystallographic refinement and structure-factor time-averaging by molecular dynamics in the absence of a physical force field Molecular Simulation. 10: 377-395. DOI: 10.1080/08927029308022174  1
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  1
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  0.72
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  1
1992 Mark AE, Van Gunsteren WF. Simulation of the thermal denaturation of hen egg white lysozyme: Trapping the molten globule state Biochemistry. 31: 7745-7748. PMID 1510961 DOI: 10.1021/BI00149A001  1
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  0.72
1992 van Gunsteren WF, Mark AE. Prediction of the activity and stability effects of site-directed mutagenesis on a protein core Journal of Molecular Biology. 227: 389-395. PMID 1404360 DOI: 10.1016/0022-2836(92)90895-Q  1
1992 Müller-Plathe F, Rogers SC, van Gunsteren WF. Computational evidence for anomalous diffusion of small molecules in amorphous polymers Chemical Physics Letters. 199: 237-243. DOI: 10.1016/0009-2614(92)80112-O  1
1990 Gros P, van Gunsteren WF, Hol WG. Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. Science (New York, N.Y.). 249: 1149-52. PMID 2396108 DOI: 10.1126/Science.2396108  0.44
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  1
1989 Lautz J, Kessler H, Blaney JM, Scheek RM, Van Gunsteren WF. Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin A. International Journal of Peptide and Protein Research. 33: 281-8. PMID 2753598  1
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  1
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  1
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  1
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  1
1988 Shi YY, Yun RH, van Gunsteren WF. Molecular dynamics simulation of despentapeptide insulin in a crystalline environment. Journal of Molecular Biology. 200: 571-7. PMID 3294422 DOI: 10.1016/0022-2836(88)90543-8  0.6
1988 Kaptein R, Boelens R, Scheek RM, van Gunsteren WF. Protein structures from NMR. Biochemistry. 27: 5389-95. PMID 3052574 DOI: 10.1021/Bi00415A001  1
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  1
1987 Lautz J, Kessler H, Boelens R, Kaptein R, van Gunsteren WF. Conformational analysis of a cyclic thymopoietin-analogue by 1H n.m.r. spectroscopy and restrained molecular dynamics simulations. International Journal of Peptide and Protein Research. 30: 404-14. PMID 3692686 DOI: 10.1111/J.1399-3011.1987.Tb03348.X  0.76
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  0.72
1986 Sandblom P, Åqvist J, Jones TA, Newcomer ME, van Gunsteren WF, Tapia O. Structural changes in retinol binding protein induced by retinol removal. A molecular dynamics study Biochemical and Biophysical Research Communications. 139: 564-570. PMID 3767978 DOI: 10.1016/S0006-291X(86)80028-6  1
1986 Åqvist J, Sandblom P, Jones TA, Newcomer ME, van Gunsteren WF, 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. 192: 593-603. PMID 3560228 DOI: 10.1016/0022-2836(86)90279-2  1
1985 Zuiderweg ER, Scheek RM, Boelens R, van Gunsteren WF, Kaptein R. Determination of protein structures from nuclear magnetic resonance data using a restrained molecular dynamics approach: the lac repressor DNA binding domain. Biochimie. 67: 707-15. PMID 3910108 DOI: 10.1016/S0300-9084(85)80158-9  0.76
1985 Kaptein R, Zuiderweg ER, Scheek RM, Boelens R, van Gunsteren WF. A protein structure from nuclear magnetic resonance data. lac repressor headpiece. Journal of Molecular Biology. 182: 179-82. PMID 3889346 DOI: 10.1016/0022-2836(85)90036-1  0.76
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  0.72
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  0.72
1982 Van Gunsteren WF, Berendsen HJ. Molecular dynamics: perspective for complex systems. Biochemical Society Transactions. 10: 301-5. PMID 7141081 DOI: 10.1042/BST0100301  0.72
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