Deriving Structural Information from Experimentally Measured Data on Biomolecules.Angewandte Chemie - International Edition 55.52: 15990-16010.
Publications in the field of Molecular Dynamics and Biomolecular Theory by W.F. van Gunsteren/P.H. Hünenberger (ETH Zürich), A.E. Mark (University of Queensland, AUS), S.J. Marrink/A.H. de Vries (University of Groningen, NL) and co-workers
General Reviews and Opinion Pieces
W. F. van Gunsteren, The Seven Sins in Academic Behavior in the Natural Sciences (PDF, 275 KB)
Angew. Chem. Int. Ed., 52, 118 (2013).
W. F. van Gunsteren, On the Pitfalls of Peer Review (PDF, 236 KB)
F1000Research, 4, 1244 (2015).
W. F. van Gunsteren, Going for a PhD: Joy and Pitfalls
Helv. Chim. Acta, 99, 1 (2016)
W. F. van Gunsteren, Publication of Research Results: Use and Abuse (PDF, 159 KB)
Publications since 2003
Publication of Research Results: Use and Abuse.Infozine S1: 27-28.
Going for a PhD: Joys and Pitfalls.Helvetica Chimica Acta 99.10: 755-759.
On the use of time-averaging restraints when deriving biomolecular structure from 3J-coupling values obtained from NMR experiments.Journal of Biomolecular NMR 66.1: 69-83.
Investigation of the structural preference and flexibility of the loop residues in amyloid fibrils of the HET-s prion.Physical Chemistry, Chemical Physics 18.8: 5860-5866.
A comparison of pathway-independent and pathway-dependent methods in the calculation of conformational free enthalpy differences.Protein Science 25.1: 184-191.
GROMOS polarisable model for acetone.Molecular Physics 114.6: 845-854.
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 and Medicinal Chemistry 24.20: 4936-4948.
Flexible Boundaries for Multiresolution Solvation: An Algorithm for Spatial Multiscaling in Molecular Dynamics Simulations.Journal of Chemical Theory and Computation 11.11: 5447-5463.
Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase.Journal of Chemical Theory and Computation 11.7: 2925-2937.
On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations.The Journal of Chemical Physics 143.3: 034110.
Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane.Journal of Computational Chemistry 36.17: 1311-1321.
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 11.5: 1983-1986.
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 (BBA). General subjects 1850.5: 983-995.
Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations.European Biophysics Journal 44.4: 235-247.
Challenge of Representing Entropy at Different Levels of Resolution in Molecular Simulation.Journal of Physical Chemistry B 119.3: 753-763.
Structural and energetic effects of the use of polarisable water to solvate proteins.Molecular Physics 113.17-18: 2815-2828.
On the pitfalls of peer review.F1000Research 4: 1244.
GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.Journal of Chemical Physics 142.9: 094117.
An improved simple polarisable water model for use in biomolecular simulation.The journal of chemical physics 141: 22D515.
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation.PLoS computational biology 10.12: e1003995.
Time-averaged order parameter restraints in molecular dynamics simulations.Journal of biomolecular NMR 60.2-3: 169-187.
Polarizable Model for DMSO and DMSO-Water Mixtures.The journal of physical chemistry. B 118.34: 10175-10186.
Use of Enveloping Distribution Sampling to Evaluate Important Characteristics of Biomolecular Force Fields.The journal of physical chemistry. B 118.24: 6424-6430.
Rapid sampling of folding equilibria of β-peptides in methanol using a supramolecular solvent model.Journal of chemical theory and computation 10.6: 2213-2223.
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.
Use of enveloping distribution sampling to evaluate important characteristics of biomolecular force fields.The journal of physical chemistry B 118.24: 6424-6430.
Refinement of the Application of the GROMOS 54A7 Force Field to β-Peptides.Journal of computational chemistry 34.32: 2796-2805.
Enhanced conformational sampling using enveloping distribution sampling.Journal of chemical physics 139.14: 144105.
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 117.39: 11433-11447.
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 111.14-15: 2334-2344.
The effect of branched side chains on the relative stability of alpha- and pi-helices: a combination of the enveloping distribution sampling and one-step perturbation methods.Molecular physics 111.14-15: 2126-2130.
Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation.Journal of computational chemistry 34.22: 1899-1906.
Molecular Dynamics Simulations of Barley and Maize Lipid Transfer Proteins Show Different Ligand Binding Preferences in Agreement with Experimental Data.Biochemistry 52.30: 5029-5038.
Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: A molecular dynamics study of cellobiose stereoisomers.European biophysics journal 42.7: 521-537.
Exploration of swapping enzymatic function between two proteins: A simulation study of chorismate mutase and isochorismate pyruvate lyase.Protein science 22.6: 809-822.
On the use of advanced modelling techniques to investigate the conformational discrepancy between two X-ray structures of the AppA BLUF domain.Molecular simulation 39.6: 472-486.
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 9.3: 1334-1346.
Multi-Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues.Angewandte Chemie-International Edition 52.10: 2820-2834.
Conformational Preferences of a beta-Octapeptide as Function of Solvent and Force-Field Parameters.Helvetica chimica acta 96.2: 189-200.
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 34.5: 387-393.
The Seven Sins in Academic Behavior in the Natural Sciences.Angewandte Chemie. International edition in English 52.1: 118-122.
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 : JCTC 10.1: 391-400.
Multi-Resolution Simulation in Biochemistry: Methodological Issues and Exploration of Peptide Folding and the Origins of Differential Catalysis Observed between Two Structurally Similar Enzymes.Biophysical journal 104.2: 212A-212A.
Relative Free Enthalpies for Point Mutations in Two Proteins with Highly Similar Sequences but Different Folds.Biochemistry 52.29: 4962-4970.
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 9.1: 126-134.
Free Enthalpy Differences between alpha-, pi-, 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 9.3: 1328-1333.
Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code.PLoS genetics 9.1: e1003187.
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 52.40: 7099-7113.
Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12.Protein science 22.1: 56-64.
Validation of the GROMOS 54A7 Force Field Regarding Mixed alpha/beta-Peptide Molecules.Helvetica chimica acta 95.12: 2562-2577.
Free enthalpies of replacing water molecules in protein binding pockets.Journal of computer-aided molecular design 26.12: 1293-1309.
Free enthalpies of replacing water molecules in protein binding pockets.Journal of computer-aided molecular design 26.12: 1293-1309.
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 21.11: 1672-1681.
Influence of 63Ser Phosphorylation and Dephosphorylation on the Structure of the Stathmin Helical Nucleation Sequence: A Molecular Dynamics Study.Biochemistry 51.42: 8455-8463.
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 33.24: 1907-1917.
Molecular dynamics simulation of thionated hen egg white lysozyme.Protein Science 21.8: 1153-1161.
Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.Journal of Chemical Theory and Computation 8.7: 2391-2403.
Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system.Journal of Chemical Physics 137.4: 044120.
On the calculation of (3)J(alpha beta)-coupling constants for side chains in proteins.Journal of Biomolecular Nmr 53.3: 223-246.
An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.European biophysics journal 41.7: 579-595.
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9.Journal of Computational Chemistry 33.17: 1467-1477.
Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation.Computer physics communications 183.4: 890-903.
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 33.6: 640-651.
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 33.4: 363-378.
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol.The journal of chemical physics 136.5: ARTN 054505.
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 279.2: 299-315.
Thirty-five years of biomolecular simulation: Development of methodology, force fields and software.Molecular simulation 38.14-15: 1271-1281.
Exploring the properties of small molecule protein binding via molecular simulations: the TRSH–p53 core domain complex.Molecular biosystems 8.11: 2891-2900.
New functionalities in the GROMOS biomolecular simulation software.Journal of computational chemistry 33.3: 340-353.
Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution.Journal of Chemical Physics 137.6: 064108.
Helical Content of a β3-Octapeptide in Methanol: Molecular Dynamics Simulations Explain a Seeming Discrepancy between Conclusions Derived from CD and NMR Data.Chemistry 18.2: 586-593.
On developing coarse-grained models for biomolecular simulation: A review.Physical chemistry, chemical physics 14.36: 12423-12430.
Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.European biophysics journal 41.8: 647-661.
Recent advances in computational actinoid chemistry.Chemical Society Reviews 41.17: 5836-5865.
Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: Enthalpic and entropic driving forces.ChemPhysChem 12.17: 3214-3223.
On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, α-, and л-Helices.Journal of chemical theory and computation 7.12: 3884-3897.
An effective force field for molecular dynamics simulations of dimethyl sulfone.Molecular Physics 109.22: 2593-2605.
Biomolecular structure refinement using the GROMOS simulation software.Journal of biomolecular NMR 51.3: 265-281.
A Method for Conformational Sampling of Loops in Proteins Based on Adiabatic Decoupling and Temperature or Force Scaling.ChemPhysChem 12.14: 2609-2614.
Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling.The journal of chemical physics 135.10: 104106.
Free energy calculations offer insights into the influence of receptor flexibility on ligand–receptor binding affinities.Journal of computer-aided molecular design 25.8: 709-716.
Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures.Journal of molecular biology 411.1: 286-297.
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 32.10: 2290-2297.
Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.The journal of chemical physics 135.2: 024105.
Recent Advances in Computational Actinide Chemistry.Huaxue-jinzhan = Progress in chemistry 23.7: 1566-1581.
Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding.Journal of chemical theory and computation 7.5: 1237-1243.
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 7.4: 1032-1044.
Enhancing the Configurational Sampling of Ions in Aqueous Solution Using Adiabatic Decoupling with Translational Temperature Scaling.The Journal of Physical Chemistry B 115.12: 2931-2936.
Membrane protein dynamics in different environments: Simulation study of the outer membrane protein X in a lipid bilayer and in a micelle.European Biophyisics Journal 40.1: 39-58.
GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories.Journal of chemical theory and computation 7.10: 3379-3390.
The effect of using a polarizable solvent model upon the folding equilibrium of different -peptides.Molecular physics 109.4: 493-506.
On the Calculation of the Dielectric Permittivity and Relaxation of Molecular Models in the Liquid Phase.Journal of chemical theory and computation 7.5: 1469-1475.
A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability.Protein science 19.11: 2186-2195.
Using One-Step Perturbation to Predict the Effect of Changing Force-Field Parameters on the Simulated Folding Equilibrium of a β-Peptide in Solution.Journal of computational chemistry 31.13: 2419-2427.
The Propensity of -Aminoisobutyric Acid (=2-Methylalanine; Aib) to Induce Helical Secondary Structure in an -Heptapeptide: A Computational Study.Helvetica chimica acta 93.8: 1513-1531.
A one-site polarizable model for liquid chloroform: COS/C.Molecular physics 108.13: 1749-1757.
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 6.6: 1783-1797.
Basic ingredients of free energy calculations: A review.Journal of computational chemistry 31.8: 1569-1582.
Feature Article Basic Ingredients of Free Energy Calculations: A Review.Journal of computational chemistry 31.8: 1569-1582.
Structure Determination of a Flexible Cyclic Peptide Based on NMR and MD Simulation (3)J-Coupling.ChemPhysChem 11.4: 830-835.
Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: Preferential affinity/exclusion effects and their relevance for bioprotection.Molecular simulation 36.9: 708-728.
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.Physical chemistry, chemical physics 12.9: 2257-2258.
Comparing geometric and kinetic cluster algorithms for molecular simulation data.The journal of chemical physics 132.7: 074110.
What stabilizes the 3(14)-helix in β(3)-peptides?: A conformational analysis using molecular simulation.Proteins 78.7: 1677-1690.
Prediction of Folding Equilibria of Differently Substituted Peptides Using One-Step Perturbation.Journal of the American Chemical Society 132.21: 7276-7278.
A New Force Field for Simulating Phosphatidylcholine Bilayers.Journal of computational chemistry 31.6: 1117-1125.
A GPU Solvent-Solvent Interaction Calculation Accelerator for Biomolecular Simulations Using the GROMOS Software.Journal of computational chemistry 31.8: 1636-1643.
The thermal isomerization of the GFP chromophore: A computational study.Physical chemistry, chemical physics 12.36: 11051-11061.
Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations.Protein science 18.10: 2090-2099.
Force-field dependence of the conformational properties of α, ω-dimethoxypolyethylene glycol.Molecular physics 107.13: 1313-1321.
Interpreting experimental data by using molecular simulation instead of model building.Chemistry 15.26: 6389-6398.
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.The journal of chemical physics 130.21: 214904.
A Method to Explore Protein Side Chain Conformational Variability Using Experimental Data.ChemPhysChem 10.18: 3213-3228.
Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.Journal of computational chemistry : organic - inorganic - physical - biological 30.11: 1664-1679.
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 : JCTC 5.2: 276-286.
Influence of Backbone Fluorine Substitution upon the Folding Equilibrium of a β-Heptapeptide.The journal of physical chemistry. B 113.25: 8695-8703.
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase.Journal of computational chemistry 30.4: 514-523.
Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D.The journal of physical chemistry. A 113.43: 11570-11579.
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 10.10: 1657-1665.
Exact distances and internal dynamics of perdeuterated ubiquitin from NOE buildups.Journal of the American Chemical Society 131.47: 17215-17225.
Folding and unfolding of two mixed alpha/beta peptides.ChemBioChem 10.12: 2032-2041.
On the conformational properties of amylose and cellulose oligomers in solution.International journal of carbohydrate chemistry 2009: 307695.
On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models.Physical chemistry, chemical physics 11: 1934-1941.
Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.Chemistry 14.16: 5039-5046.
Zwei der ERC- Advanced Grants 2008 gehen an Forschungsgruppen des LPC im D- CHAB: Neue Erkenntnisse zu biomolekularen Systemen und kalten Atomen & Molekülen.Molekül 2008.18: 4-4.
Simulation of the Outer Membrane Protein X in a Lipid Bilayer and in a Micelle.Paper presented at the From Computational Biophysics to Systems Biology (CBSB08), Jülich, Germany, May 19-21.
Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions.The journal of chemical physics 128.17: 174112-1-174112-12.
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.Journal of computational chemistry 29.2: 157-166.
Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: A MD simulation study.ChemBioChem 9.11: 1749-1756.
Exploring the conserved water site and hydration of a coiled-coil trimerization motif: a MD simulation study.ChemBioChem : a European journal of chemical biology 9.11: 1749-1756.
A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pH.ChemBioChem 9.6: 923-933.
Molecular dynamics study of beta-peptides.Journal of peptide science 14.8: 167-167.
QM–MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians.Physical chemistry, chemical physics 10.2: 297-302.
Molecular simulation as an aid to experimentalists.Current opinion in structural biology 18.2: 149-153.
Biomolecular simulation: Historical picture and future perspectives.Biochemical Society transactions 36.1: 11-15.
Computer simulation of biomolecular systems: Where do we stand?Paper presented at the NIC Workshop 2008, Jülich, Germany, May 19-21.
COMP 39-Force-field development for computer simulation of biomolecular systems: The GROMOS case.Paper presented at the 236th National Meeting of the American-Chemical-Society, Philadelphia, PA, USA, August 17-21.
CSE Annual Report 2007/2008: July 2007 to July 2008.
Disulfide Bond Shuffling in Bovine alpha-Lactalbumin: MD Simulation Confirms Experiment.Biochemistry 47.46: 12104-12107.
Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase.Biochemistry 47.9: 2945-2951.
Atomic Models of De Novo Designed ccβ-Met Amyloid-Like Fibrils.Journal of molecular biology 376.3: 898-912.
Use of Molecular-Dynamics Simulation for Optimizing Protein Stability: Consensus-Designed Ankyrin Repeat Proteins.Helvetica chimica acta 91.9: 1605-1613.
Structure and dynamics of two β-peptides in solution from molecular dynamics simulations validated against experiment.European biophysics journal 37.6: 903-912.
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 3.4: 1499-1509.
Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water.Biophysical journal 93.2: 442-455.
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 111.23: 6425-6436.
Enveloping distribution sampling: A method to calculate free energy differences from a single simulation.The journal of chemical physics 126.18: ARTN 184110.
Comparison of thermodynamic properties of coarse-grained and atomic-level simulaton models.ChemPhysChem 8.3: 452-461.
Enveloping distribution sampling: A method to calculate free energy differences from a single simulation.The journal of chemical physics 126.18: 184110-1-184110-10.
Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations.ChemPhysChem 8.10: 1557-1564.
Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.Journal of biomolecular NMR 39.4: 265-273.
On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm.The journal of chemical physics 127.18: 184102-1-184102-8.
Comparison of estimates of free energy for binding of mono- and di-substituted benzenes with alpha-cyclodextrin obtained by single-step perturbation and thermodynamic integration.Paper presented at the 13th International Cyclodextrin Symposium, Torino, Italy, May 14-17.
Simulation of beta-depsipeptides: The effect of missing hydrogen-bond donors on their folding equilibria.Biopolymers 85.4: 318-332.
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 105.13-14: 1861-1881.
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 3.6: 2128-2137.
Simulation of folding equilibria.In Foldamers : Structure, Properties and Applications, edited by Stefan Hecht and Ivan Huc, 173-192. Weinheim: Wiley-VCH.
Analysis of the driving forces for biomolecular solvation and association.Paper presented at the International School of Physics, Varenna, Italy, July 4-14.
On using oscillating time-dependent restraints in MD simulation.Journal of biomolecular NMR 37.1: 1-14.
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 16.6: 1101-1118.
Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.Protein science 16.7: 1349-1359.
Applications of molecular dynamics simulations in drug design.In Comprehensive medicinal chemistry II. 4, Computer-assisted drug design, edited by Jonathan S. Mason, 651-668. Amsterdam: Elsevier.
Folding-Unfolding Equilibrium of a Methylidene-Substituted β-Peptide.Helvetica chimica acta 90.10: 1966-1979.
Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA.Biochemistry 46.22: 6500-6512.
Analysis of neo-pentane-urea pair potentials of mean force in aqueous urea.Molecular physics 105.1: 33-39.
A comparison of methods to compute a potential of mean force.ChemPhysChem 8.1: 162-169.
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 33.14: 1143-1154.
Computational analysis of the mechanism and thermodynamics of inhibition of phosphodiesterase 5A by synthetic ligands.Journal of chemical theory and computation : JCTC 3.1: 301-311.
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 83.6: 636-645.
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 bioinformatics 65.3: 702-711.
Pathway dependence of the efficiency of calculating free energy and entropy of solute-solute association in water.Chemical physics 330.3: 410-416.
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins.Proteins 65.2: 285-295.
Protein under pressure: Molecular dynamics simulation of the arc repressor.Proteins 65.1: 136-144.
Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.Biophysical journal 91.4: 1460-1470.
Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations.The journal of physical chemistry. B 110.31: 15602-15614.
Enthalpy-entropy compensation in the effects of urea on hydrophobic interactions.The journal of physical chemistry. B 110.26: 12852-12855.
Conformational and dynamical properties of disaccharides in water: A molecular dynamics study.Biophysical journal 90.12: 4337-4344.
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 : organic - inorganic - physical - biological 27.7: 857-867.
Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates.The journal of physical chemistry. B 110.16: 8464-8473.
Multigraining: An algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.The journal of chemical physics 124.15: 154106.
Sampling of rare events using hidden restraints.The journal of physical chemistry. B 110.16: 8488-8498.
Terminal-group effects on the folding behavior of selected beta-peptides.Proteins : structure, function, and bioinformatics 63.1: 136-143.
Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?Proteins : structure, function, and bioinformatics 63.1: 210-218.
Force field evaluation for biomolecular simulation: Free enthalpies of solvation of polar and apolar compounds in various solvents.ChemPhysChem : a European journal of chemical physics and physical chemistry 7.3: 671-678.
Calculating zeros: Non-equilibrium free energy calculations.Chemical physics 323.1: 102-108.
Acetonitrile revisited: A molecular dynamics study of the liquid phase.Molecular physics 104.3: 477-483.
A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer.European biophysics journal 35.3: 255-267.
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 128.1: 159-170.
Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer.Chemistry : a European journal 12.1: 72-75.
Numerical simulation of the pressure denaturation of a helical beta-peptide heptamer solvated in methanol.Helvetica chimica acta 89.3: 475-482.
Biomolecular modeling: Goals, problems, perspectives.Angewandte Chemie. International edition in English 45.25: 4064-4092.
Biomolecular modelling: Goals, problems, perspectives.Angewandte Chemie 45.25: 4064-4092.
Biomolekulare Modellierung: Ziele, Probleme, Perspektiven.Angewandte Chemie 118.25: 4168-4198.
CSE Annual Report 2005/2006: July 2005 to July 2006.
Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: Pathway prediction and reconciliation of X-ray crystallographic and NMR solution data.Protein science 15.11: 2544-2551.
Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.Journal of computational chemistry 27.13: 1494-1504.
The GROMOS software for biomolecular simulation: GROMOS05.Journal of computational chemistry 26.16: 1719-1751.
On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: A molecular dynamics simulation study.Chemistry : a European journal 11.24: 7276-7293.
Accounting for polarization in molecular simulation.Computer physics communications 172.2: 69-85.
Interpreting NMR Data for β-Peptides Using Molecular Dynamics Simulations.Journal of the American Chemical Society 127.41: 14320-14329.
Amine hydration: A united-atom force-field solution.ChemPhysChem 6.9: 1800-1804.
Molecular-Dynamics Simulations of C- and N-Terminal Peptide Derivatives of GCN4-p1 in Aqueous Solution.Chemistry & biodiversity 2.8: 1086-1104.
Unusual compactness of a polyproline type II structure.Proceedings of the National Academy of Sciences of the United States of America 102.33: 11698-11703.
Molecular dynamics simulation of lipid bilayers with GROMOS96: Application of surface tension.Molecular simulation 31.8: 543-548.
Efficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations.Chemistry 11.15: 4340-4348.
The relative stability of homochiral and heterochiral alanine dipeptides. Effects of perturbation pathways and force-field parameters on free energy calculations.Paper presented at the IUBMB 50th Anniversary Symposium, Budapest, Hungary, July 2-7.
Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations.Molecular physics 103.14: 1961-1969.
An improved nucleic acid parameter set for the GROMOS force field.Journal of computational chemistry 26.7: 725-737.
An approximate but fast method to impose flexible distance constraints in molecular dynamics simulations.The journal of chemical physics 122.14: 144106.
Use of Molecular Dynamics in the Design and Structure Determination of a Photoinducible β-Hairpin.Journal of the American Chemical Society 127.13: 4935-4942.
A Photoinducible β-Hairpin.Journal of the American Chemical Society 127.9: 2929-2936.
Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations.Proteins : structure, function, and bioinformatics 58.2: 439-449.
Principles of carbopeptoid folding: A molecular dynamics simulation study.Journal of peptide science 11.2: 74-84.
Calculation of the redox potential of the protein azurin and some mutants.ChemBioChem : a European journal of chemical biology 6.4: 738-746.
Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site.Nucleic acids research 33.2: 725-733.
Biomolecular simulation: Some achievements and challenges.Annual Report of the CSE Computational Science and Engineering 200/2005: 23-43.
Entropy Calculation of HIV-1 Env gp120, its Receptor CD4, and their Complex: An Analysis of Configurational Entropy Changes upon Complexation.Biophysical journal 88.1: 15-24.
Free energies of ligand binding for structurally diverse compounds.Proceedings of the National Academy of Sciences of the United States of America : PNAS 102.19: 6750-6754.
Methane clustering in explicit water: Effect of urea on hydrophobic interactions.Physical chemistry, chemical physics : PCCP : a journal of European Chemical Societies 7.1: 53-58.
Validation of the 53A6 GROMOS force field.European biophysics journal : with biophysics letters 34.4: 273-284.
Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time.The journal of physical chemistry. B 109.23: 11643-11652.
Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme.Journal of biomolecular NMR 30.4: 407-422.
Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice.The journal of chemical physics 121.19: 9549-9564.
Simulation of the Substrate Cavity Dynamics of Quercetinase.Journal of molecular biology 344.3: 725-738.
Do valine side chains have an influence on the folding behavior of beta-substituted beta-peptides?Helvetica chimica acta 87.10: 2487-2506.
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 25.13: 1656-1676.
beta-Hairpin folding and stability: Molecular dynamics simulations of designed peptides in aqueous solutions.Journal of peptide science 10.9: 546-565.
Carbopeptoid folding: Effects of stereochemistry, chain length, and solvent.Angewandte Chemie 43.31: 4055-4059.
Alpha- and beta-polypeptides show a different stability of helical secondary structure.Tetrahedron : the international journal for the rapid publication of critical reviews and original research communications in organic chemistry 60.35: 7775-7780.
Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: A molecular dynamics study.Carbohydrate research 339.10: 1697-1709.
Comparison of properties of aib-rich peptides in crystal and solution: A molecular dynamics study.ChemPhysChem 5.5: 633-641.
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 1.3: 505-519.
Simulating the physiological phase of hydrated DPPC bilayers: The ester moiety.Soft materials 2.1: 27-45.
Estimating entropies from molecular dynamics simulations.The journal of chemical physics 120.6: 2652-2661.
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation.Proteins : structure, function, and bioinformatics 54.2: 237-246.
An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures.The journal of physical chemistry B 108.4: 1436-1445.
On the transferability of the SPCAL water model to biomolecular simulation.Brazilian journal of physics 34.1: 116-125.
Are NMR-derived model structures for beta-peptides representative for the ensemble of structures adopted in solution?Angewandte Chemie. International edition in English 43.46: 6312-6316.
Computer simulation of urea-water mixtures: A test of force field parameters for use in biomolecular simulation.The journal of physical chemistry B 108.3: 1065-1071.
Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9 M aqueous urea solution.Physical chemistry, chemical physics 6.4: 697-702.
Entropic contributions in cosolvent binding to hydrophobic solutes in water.The journal of physical chemistry B 108.3: 1056-1064.
Energy–Entropy Compensation in the Transfer of Nonpolar Solutes from Water to Cosolvent/Water Mixtures.ChemPhysChem 5.1: 144-147.
Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding.Proteins 54.1: 116-127.
Circular dichroism spectra of beta-peptides: Sensitivity to molecular structure and effects of motional averaging.European biophysics journal 32.8: 661-670.
Molecular Dynamics Simulations of Small Peptides: Can One Derive Conformational Preferences from ROESY Spectra?Chemistry : a European journal 9.23: 5838-5849.
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character.Journal of computational chemistry 24.14: 1730-1739.
A novel approach for designing simple point charge models for liquid water with three interaction sites.Journal of computational chemistry 24.9: 1087-1096.
A consistent potential energy parameter set for lipids: Dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field.European biophysics journal : with biophysics letters 32.1: 67-77.
Increasing the time step and efficiency of molecular dynamics simulations: Optimal solutions for equilibrium simulations or structure refinement of large biomolecules.Molecular simulation 29.2: 123-138.
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 119.23: 12205-12223.
Development of a simple, self-consistent polarizable model for liquid water.The journal of chemical physics 118.1: 221-234.
Molecular Dynamics Simulation of n-Dodecylphosphate Aggregate Structures.European Biophysics Journal 30.5: 330-343.