Research Topics
Genomes and Genes | Wilfred F van GunsterenSummaryAffiliation: Swiss Federal Institute of Technology Country: Switzerland Publications
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Detail Information
Publications
Biomolecular structure refinement based on adaptive restraints using local-elevation simulationMarkus Christen
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zurich, 8093 Zurich, Switzerland
J Biomol NMR 39:265-73. 2007..Afterwards the torsional angles varphi are kept restrained by the built-up local-elevation potential energies...
On developing coarse-grained models for biomolecular simulation: a reviewSereina Riniker
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
Phys Chem Chem Phys 14:12423-30. 2012..e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest...- Molecular simulation as an aid to experimentalistsWilfred F van Gunsteren
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
Curr Opin Struct Biol 18:149-53. 2008..A critical analysis of the various factors that may influence the apparent degree of agreement between the results of simulations and experimentally measured quantities is presented and illustrated using examples from recent literature... - Biomolecular simulation: historical picture and future perspectivesWilfred F van Gunsteren
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, CH 8093 Zurich, Switzerland
Biochem Soc Trans 36:11-5. 2008..Progress over the last 30 years is sketched and perspectives are outlined for the future... - The thermal isomerization of the GFP chromophore: A computational studyDongqi Wang
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093, Zurich, Switzerland
Phys Chem Chem Phys 12:11051-61. 2010..Our study suggests that the ability of a nucleophile to assist the thermal isomerization of HOBDI mainly depends on its ability to give a proton upon the addition of the nucleophile to the substrate... - Biomolecular modeling: Goals, problems, perspectivesWilfred F van Gunsteren
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
Angew Chem Int Ed Engl 45:4064-92. 2006..These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling... - Validation of the 53A6 GROMOS force fieldChris Oostenbrink
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
Eur Biophys J 34:273-84. 2005..The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized... - Terminal-group effects on the folding behavior of selected beta-peptidesPeter J Gee
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
Proteins 63:136-43. 2006..The simulated motions bear out empirical observations as to the effect of chemical protection of terminal groups on the stability of beta-peptide helical folds and they support the hypothesis of charge-dipole stabilization... - 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 methanolBruno A C Horta
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
J Comput Chem 33:1907-17. 2012.... - Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?Bojan Zagrovic
Department of Chemistry and Applied Biosciences, ETH Honggerberg, Zurich, Switzerland
Proteins 63:210-8. 2006..In light of the examples given, we conclude that comparing experimental NOE distance restraints with large simulated ensembles provides just by itself only limited information about the quality of simulation... - A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayerAlice Glättli
Laboratorium fur Physikalische Chemie, Swiss Federal Institute of Technology, ETH Hönggerberg HCI, 8093 Zurich, Switzerland
Eur Biophys J 35:255-67. 2006..In addition, peptide-lipid interactions were investigated showing that the C-terminus of the peptide provides an anchor to the lipid bilayer by forming hydrogen bonds with the lipid head groups... 
Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamicsDavid B Kony
Laboratory of Physical Chemistry, ETH Zurich, CH 8093 Zurich, Switzerland
Protein Sci 16:1101-18. 2007....- The GROMOS software for biomolecular simulation: GROMOS05Markus Christen
Laboratory of Physical Chemistry, , , , Switzerland
J Comput Chem 26:1719-51. 2005..The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented... - An improved nucleic acid parameter set for the GROMOS force fieldThereza A Soares
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, , 8093 Zurich, Switzerland
J Comput Chem 26:725-37. 2005..The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves... - Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinitiesJozica Dolenc
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
J Comput Aided Mol Des 25:709-16. 2011..The differences in the free enthalpy of binding do not arise only from the changes in ligand-DNA interactions but also from changes in ligand-solvent interactions as well as from the loss of DNA configurational entropy upon restraining... - Folding and unfolding of two mixed alpha/beta peptidesDongqi Wang
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich Switzerland
Chembiochem 10:2032-41. 2009..We conclude that our simulations are complementary to the experiments by providing detailed information on the conformational distributions... - Free energies of ligand binding for structurally diverse compoundsChris Oostenbrink
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, , CH-8093 Zurich, Switzerland
Proc Natl Acad Sci U S A 102:6750-4. 2005..The free-energy calculations can be straightforwardly parallelized, allowing for an efficient means to understand and predict relative binding free energies... - Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics studyHaibo Yu
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, , , Switzerland
Chemphyschem 5:633-41. 2004.... - Biomolecular structure refinement using the GROMOS simulation softwareNathan Schmid
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
J Biomol NMR 51:265-81. 2011.... - Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS softwareSereina Riniker
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
J Phys Chem B 115:13570-7. 2011..Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given... - Protein under pressure: molecular dynamics simulation of the arc repressorDaniel Trzesniak
Laboratory of Physical Chemistry, , , Switzerland
Proteins 65:136-44. 2006..Also, the onset of denaturation of the separated chains was observed... - Comparison of thermodynamic properties of coarse-grained and atomic-level simulation modelsRiccardo Baron
Laboratorium fur Physikalische Chemie, ETH, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
Chemphyschem 8:452-61. 2007..However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties... - Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibriaZrinka Gattin
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
Biopolymers 85:318-32. 2007..The simulations are complementary to the experimental data by providing detailed insight into the conformational distributions that are compatible with the experimentally measured average values of observables... - Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteinsHaibo Yu
Laboratory of Physical Chemistry, , , , Switzerland
Proteins 65:285-95. 2006..The simulation trajectories suggest that the stability of the designed AR proteins can be increased by optimizing the electrostatic interactions within and between the different repeats... - Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parametersDaan P Geerke
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, CH 8093 Zurich, Switzerland
J Phys Chem B 111:6425-36. 2007.... - Conformational and dynamical properties of disaccharides in water: a molecular dynamics studyCristina S Pereira
Laboratory of Physical Chemistry, , , Switzerland
Biophys J 90:4337-44. 2006.... - Circular dichroism spectra of beta-peptides: sensitivity to molecular structure and effects of motional averagingXavier Daura
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, , 8093 Zurich, Switzerland
Eur Biophys J 32:661-70. 2003..This indicates that the CD spectra of these peptides are very sensitive to small local structural differences... - A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6Chris Oostenbrink
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, , , Switzerland
J Comput Chem 25:1656-76. 2004..The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed... - On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation studyAlice Glättli
Laboratorium fur Physikalische Chemie, Swiss Federal Institute of Technology, ETH Honggerberg, HCI, 8093 Zurich, Switzerland
Chemistry 11:7276-93. 2005..In water, where the solvent competes with the solute-solute polar interactions, the folding process to the 3(14)-helix is faster in the simulations... - Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solutionNiels Hansen
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zurich CH 8093, Switzerland
J Comput Chem 33:640-51. 2012.... - Simulation of an all-beta 3-icosapeptide containing the 20 proteinogenic side chains: effect of temperature, pH, counterions, solvent, and force field on helix stabilityDaniel Trzesniak
Laboratory of Physical Chemistry, , ETH, , Switzerland
Biopolymers 83:636-45. 2006..We further investigate the reasons for the 3(14)-helix stability/instability in methanol/water. Of all factors studied, the presence of counterions seems to be the one inducing most significant effects in the simulations... - Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamerPeter J Gee
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, , Switzerland
Chemistry 12:72-5. 2005.... - Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation studyJozica Dolenc
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
Chembiochem 9:1749-56. 2008..Together, our study contributes to understanding the principles of three-stranded coiled-coil formation... - On the calculation of ³Jαβ-coupling constants for side chains in proteinsDenise Steiner
Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
J Biomol NMR 53:223-46. 2012..The results show that the widely used Karplus relations are only a rough estimate for the relation between (3) J (αβ)-couplings and the corresponding χ(1)-angle in proteins... - Interpreting NMR data for beta-peptides using molecular dynamics simulationsDaniel Trzesniak
Laboratory of Physical Chemistry, , , , Switzerland
J Am Chem Soc 127:14320-9. 2005..The MD conformational ensembles allowed for a detailed and consistent interpretation of the experimental data and showed the small but specific conformational differences between the protected and unprotected forms of the peptide... - New functionalities in the GROMOS biomolecular simulation softwareAnna Pitschna E Kunz
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
J Comput Chem 33:340-53. 2012..Examples that illustrate the use of these functionalities are given... - Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forcesAlexandra Choutko
Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
Chemphyschem 12:3214-23. 2011..Note that the latter effect is a generic concept and may in principle involve both a solvent release and an interaction component, depending on the solute considered... - 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 foldAndreas P Eichenberger
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
FEBS J 279:299-315. 2012..Upon esterification, the backbone-side chain and side chain-side chain hydrogen-bonding pattern of HEWL changes to maintain its compactness and thus the structural stability of the ester-linked lysozymes... - Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulationClara D Christ
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
J Comput Chem 30:1664-79. 2009..In this reference state not all barriers between all pairs of states are reduced. Instead a minimum spanning tree of states is calculated, which connects states that are "closest" in configuration space... - Interpreting experimental data by using molecular simulation instead of model buildingZrinka Gattin
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
Chemistry 15:6389-98. 2009.... - Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in waterDavid B Kony
Laboratory of Physical Chemistry, ETH Zurich, CH 8093 Zurich, Switzerland
Biophys J 93:442-55. 2007.... - Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solutionZhixiong Lin
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH 8093, Zurich, Switzerland
J Comput Chem 31:2419-27. 2010..The evaluated methodology constitutes an efficient tool in force-field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude... - Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/DAnna Pitschna E Kunz
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
J Phys Chem A 113:11570-9. 2009.... - What stabilizes the 3(14)-helix in beta3-peptides? A conformational analysis using molecular simulationBettina Keller
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zurich, CH 8093 Zurich, Switzerland
Proteins 78:1677-90. 2010..The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides... - Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulationsMarkus Christen
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
Chemphyschem 8:1557-64. 2007..7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy... - Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNANathan Schmid
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
Biochemistry 46:6500-12. 2007..Furthermore, the low-energy conformations of the complexes that were found provided additional information about the mechanism of binding... - Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding proteinDirk Bakowies
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, , Switzerland
Proteins 47:534-45. 2002..Differences between the two forms of the protein are observed and discussed... - Orientation and conformational preference of leucine-enkephalin at the surface of a hydrated dimyristoylphosphatidylcholine bilayer: NMR and MD simulationIndira Chandrasekhar
Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
J Am Chem Soc 128:159-70. 2006..The conformational behavior of lenk at the DMPC surface is compared to that in the aqueous solution, both in the neutral and in the zwitterionic forms... - Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutationIris Antes
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology-Zurich, ETH-Zentrum, 8092 Zurich, Switzerland
Eur Biophys J 31:504-20. 2002..These changes, however, differ considerably during the pRGln and pRprot simulations, providing an atomistic explanation for the enhancement of the rate constant in the Gln46 mutant... - Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein bindingHaibo Yu
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, , , Switzerland
Proteins 54:116-27. 2004..Together with the available experimental data, these simulation studies indicate that Hao-containing peptides may serve as inhibitors of beta-sheet interactions between proteins... - Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained waterSereina Riniker
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
J Phys Chem B 116:8873-9. 2012..4 to 2.0 nm... - Are NMR-derived model structures for beta-peptides representative for the ensemble of structures adopted in solution?Alice Glättli
Laboratorium fur Physikalische Chemie, ETH, ETH Honggerberg, HCI, 8093 Zurich, Switzerland
Angew Chem Int Ed Engl 43:6312-6. 2004 - Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclaseFabienne Schwab
Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Zurich, CH 8093, Switzerland
Biochemistry 47:2945-51. 2008..Detailed comparisons and potential reasons for this are given... - Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitorsSereina Riniker
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
J Chem Phys 135:024105. 2011..In addition, two different schemes to determine automatically the EDS reference state parameters and two different topology approaches are compared... - A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force fieldIndira Chandrasekhar
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Hoenggerberg, 8093, Zurich, Switzerland
Eur Biophys J 32:67-77. 2003..An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed... - Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experimentBojan Zagrovic
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
Eur Biophys J 37:903-12. 2008..The central members of all of the clusters populating more than 5% of all of the structures are shown, together with the most dominant hydrogen bonds and the corresponding percentages of cluster members containing them... - Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptideZrinka Gattin
Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
J Phys Chem B 113:8695-703. 2009..Helv. Chim. Acta 2005, 88, 266-280) may lead to molecular structures that are not representative for the ensemble of molecular conformations... - Comparing geometric and kinetic cluster algorithms for molecular simulation dataBettina Keller
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
J Chem Phys 132:074110. 2010.... - A photoinducible beta-hairpinAndreas Aemissegger
Laboratorium für Organische Chemie and Laboratorium für Physikalische Chemie, Swiss Federal Institute of Technology, ETH Honggerberg, CH 8093 Zurich, Switzerland
J Am Chem Soc 127:2929-36. 2005..These results suggest that suitably substituted azobenzenes can be used as photoinducible turn elements to investigate and control the folding and stability of beta-sheets... - Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solventsDaan P Geerke
Laboratory of Physical Chemistry, , , , Switzerland
Chemphyschem 7:671-8. 2006.... - Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution dataDaniel Trzesniak
Laboratory of Physical Chemistry, , ETH, , Switzerland
Protein Sci 15:2544-51. 2006..These results illustrate the use of MD simulation at atomic resolution to model structural transitions and to interpret experimental data... - Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable modelsHaibo Yu
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, , , Switzerland
J Comput Chem 27:1494-504. 2006..In particular, the experimental dielectric permittivity of 32 could be reproduced, which had been shown to be difficult when using nonpolarizable models... - Definition and testing of the GROMOS force-field versions 54A7 and 54B7Nathan Schmid
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
Eur Biophys J 40:843-56. 2011..The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained... - QM-MM interactions in simulations of liquid water using combined semi-empirical/classical HamiltoniansDaan P Geerke
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, Zurich, Switzerland
Phys Chem Chem Phys 10:297-302. 2008..In addition, the compatibility of OM3 with the classical Hamiltonian improves upon explicitly including electronic polarization in the MM subsystem... - Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanolJane R Allison
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
J Chem Phys 136:054505. 2012..The inclusion of polarizability greatly improves the reproduction of thermodynamic data measured experimentally and calculated from AL simulations for both the pure liquids and binary mixtures... - Current computer modeling cannot explain why two highly similar sequences fold into different structuresJane R Allison
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
Biochemistry 50:10965-73. 2011.... - 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 cellsRegula Walser
Laboratory of Physical Chemistry, , ETH-Zentrum, , Switzerland
Proteins 48:327-40. 2002..The results of the double-unit-cell simulations are closely similar to the results of the single-unit-cell simulations, and little motional correlation is found between the two unit cells... - Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamicsKatharina Meier
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich ETH, 8093 Zurich, Switzerland
J Phys Chem A 114:1852-9. 2010..Due to the high barriers to (un)folding, a folding/unfolding equilibrium could not be established... - A refined, efficient mean solvation force model that includes the interior volume contributionJane R Allison
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich, Switzerland
J Phys Chem B 115:4547-57. 2011.... - Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1Jozica Dolenc
Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
J Biomol NMR 47:221-35. 2010..e. measured NMR data... - Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulationChris Oostenbrink
Laboratory of Physical Chemistry, , , Switzerland
Proteins 54:237-46. 2004.... - Principles of carbopeptoid folding: a molecular dynamics simulation studyRiccardo Baron
, ETH, , , Switzerland
J Pept Sci 11:74-84. 2005..The simulations provide an atomic picture of molecular conformational variability that is consistent with the available experimental data... - Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNAJozica Dolenc
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH 8093 Zurich, Switzerland
J Phys Chem B 114:11164-72. 2010..Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively... - A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stabilityJane R Allison
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
Protein Sci 19:2186-95. 2010..The observed energetic and entropic differences can be traced to differences in the polarity of the solvent-accessible surface area and, in particular, the solute dipole moments, suggesting different reasons for their stability... - A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pHZrinka Gattin
Laboratory for Physical Chemistry, ETH Zurich, Hoenggerberg, HCI G236, 8093 Zurich, Switzerland
Chembiochem 9:923-33. 2008..The results show that the particular protonation states of acidic side chains in the protein interior might be crucial to properly modeling these proteins at low pH... - On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A reviewMarkus Christen
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, CH 8093 Zurich, Switzerland
J Comput Chem 29:157-66. 2008..The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest... - On using oscillating time-dependent restraints in MD simulationBettina Keller
Laboratorium fur Physikalische Chemie, ETH Zurich, Zurich, CH 8093, Switzerland
J Biomol NMR 37:1-14. 2007..The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling... - A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformationAdam Lange
Physical Chemistry, ETH Zurich, Wolfgang Pauli Strasse 10, Zurich, Switzerland
Chembiochem 10:1657-65. 2009..Simulations at different temperatures indicated that the network is highly dynamic and that it contributes to the thermostability of the HET-s(218-289) amyloids... - A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phaseIndira Chandrasekhar
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zentrum, 8092 Zurich, Switzerland
Eur Biophys J 31:89-101. 2002..The last parameter set tested, 45A3-45x12, also performs well when combined with either set of partial charges, although the system expands in the plane of the bilayer... - Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal waterDirk Bakowies
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
J Mol Biol 315:713-36. 2002..Solvent inside apo-FABP, for example, shows characteristics of a water droplet, while solvent in holo-FABP benefits from interactions with the ligand headgroup and slightly stronger interactions with protein residues... - Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulationRoland Bürgi
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
Proteins 47:469-80. 2002..The method is tested on the acidic residues of the protein hen egg white lysozyme. It is shown that small structural changes may have a big effect on the pK(A) values of titratable residues... - Can one derive the conformational preference of a beta-peptide from its CD spectrum?Alice Glättli
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
J Am Chem Soc 124:12972-8. 2002..To gain more insight into the relationship between the preferred conformation of a peptide and its CD spectrum, more accurate methods to calculate the CD spectrum for a given conformation are required... - Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics studyHaibo Yu
Laboratory of Physical Chemistry, , , , Switzerland
Carbohydr Res 339:1697-709. 2004..It was found that methylation at O-2 has the biggest effect, in agreement with experiment... - Unusual compactness of a polyproline type II structureBojan Zagrovic
Department of Chemistry, Laboratory of Physical Chemistry, , , , Switzerland
Proc Natl Acad Sci U S A 102:11698-703. 2005.... - Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulationJane R Allison
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
Biochemistry 49:6916-27. 2010.... - On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithmMichel A Cuendet
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
J Chem Phys 127:184102. 2007..We show the consequences when the system is coupled to a thermostat and a barostat... - Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulationsRiccardo Baron
, , , Switzerland
J Phys Chem B 110:15602-14. 2006..For the AL model, the correction due to mode anharmonicities is small, but the correction due to pairwise (supralinear) mode correlations is sizable... - Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulationsRicard Boned
Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
Chemistry 14:5039-46. 2008..The results illustrate the power of current molecular simulation force fields and techniques in establishing the link between thermodynamic quantities and conformational distributions... - Assessing equilibration and convergence in biomolecular simulationsLorna J Smith
Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
Proteins 48:487-96. 2002..This is particularly the case if the analysis includes a comparison of multiple trajectories calculated for the same system from different starting structures... - A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptidesK Anton Feenstra
BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands
J Biomol NMR 23:181-94. 2002.... - Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulationSofia Calero
Department of Chemical Engineering, Faculty of Science, University of Amsterdam, NL 1018 WV Amsterdam
Chem Biodivers 1:505-19. 2004..The proposed polyproline-type-II helicity appears only locally, and the peptide displays substantial flexibility. It is found that the peptide residues Lys10 to Tyr12 could be responsible for most of the specificity of the interaction... - Unfolded state of peptidesXavier Daura
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, , CH-8093 Zurich
Adv Protein Chem 62:341-60. 2002 - beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solutionClara M Santiveri
, , E-28006 Madrid, Spain
J Pept Sci 10:546-65. 2004..Nevertheless, the fine organization of the turn region appears to be a late event in the folding process... - Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexationShang Te D Hsu
Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
Biophys J 88:15-24. 2005..The configurational entropy analysis in terms of combined trajectories presented here shall potentially provide accurate estimations of thermodynamic properties of biomolecules given sufficient sampling of conformational space... - Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulationsLorna J Smith
Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, United Kingdom
Proteins 58:439-49. 2005..The results suggest that during the non-cooperative denaturation of the molten globule, secondary structure elements are stabilized by non-specific, non-native interactions... - Calculation of the redox potential of the protein azurin and some mutantsMarieke van den Bosch
Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands
Chembiochem 6:738-46. 2005..The errors in the free energies range from 1 to 10 k(B)T, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained... - 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 combinationsYu Zhou
Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
J Comput Chem 27:857-67. 2006.... - Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: comparisons of the wild-type protein, a b-type variant, and the apo stateLorna J Smith
Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
Proteins 65:702-11. 2006..In the absence of heme, in the apo state simulations, these residues form short but persistent regions of beta-sheet secondary structure. These could provide nucleation sites for the conversion to amyloid fibrils... - Configurational entropy change of netropsin and distamycin upon DNA minor-groove bindingJozica Dolenc
Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
Biophys J 91:1460-70. 2006.... - Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding siteJozica Dolenc
Faculty of Chemistry and Chemical Technology, University of Ljubljana Askerceva 5, SI-1000 Ljubljana, Slovenia
Nucleic Acids Res 33:725-33. 2005..The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding...