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Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.
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- European Biophysics Journal, 2022, v. 51, n. 3, p. 265, doi. 10.1007/s00249-022-01593-1
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On the use of intra‐molecular distance and angle constraints to lengthen the time step in molecular and stochastic dynamics simulations of proteins.
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- Proteins, 2022, v. 90, n. 2, p. 543, doi. 10.1002/prot.26251
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- Article
On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme.
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- ChemBioChem, 2021, v. 22, n. 6, p. 1049, doi. 10.1002/cbic.202000674
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On the use of 3J-coupling NMR data to derive structural information on proteins.
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- Journal of Biomolecular NMR, 2021, v. 75, n. 1, p. 39, doi. 10.1007/s10858-020-00355-5
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- Article
The Roots of Bio‐Molecular Simulation: The Eight‐Week CECAM Workshop 'Models for Protein Dynamics' of 1976.
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- Helvetica Chimica Acta, 2019, v. 102, n. 8, p. N.PAG, doi. 10.1002/hlca.201800239
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- Article
Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte.
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- Angewandte Chemie, 2018, v. 130, n. 4, p. 894, doi. 10.1002/ange.201702945
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- Article
Validation of Molecular Simulation: An Overview of Issues.
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- Angewandte Chemie International Edition, 2018, v. 57, n. 4, p. 884, doi. 10.1002/anie.201702945
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- Article
Interpretation of Seemingly Contradictory Data: Low NMR S<sup>2</sup> Order Parameters Observed in Helices and High NMR S<sup>2</sup> Order Parameters in Disordered Loops of the Protein hGH at Low pH.
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- Chemistry - A European Journal, 2017, v. 23, n. 40, p. 9585, doi. 10.1002/chem.201700896
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Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle.
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- Angewandte Chemie, 2016, v. 128, n. 52, p. 16222, doi. 10.1002/ange.201601828
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- Article
Deriving Structural Information from Experimentally Measured Data on Biomolecules.
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- Angewandte Chemie International Edition, 2016, v. 55, n. 52, p. 15990, doi. 10.1002/anie.201601828
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- Article
Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane.
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- Journal of Computational Chemistry, 2015, v. 36, n. 17, p. 1311, doi. 10.1002/jcc.23929
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- Article
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 H<sub>2</sub>O.
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- Helvetica Chimica Acta, 2014, v. 97, n. 12, p. 1591, doi. 10.1002/hlca.201400219
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- Article
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation.
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- PLoS Computational Biology, 2014, v. 10, n. 12, p. 1, doi. 10.1371/journal.pcbi.1003995
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A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons.
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- Journal of Computational Chemistry, 2014, v. 35, n. 10, p. 789, doi. 10.1002/jcc.23551
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- Article
Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation.
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- Journal of Computational Chemistry, 2013, v. 34, n. 22, p. 1899, doi. 10.1002/jcc.23331
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- Article
Biomolekulare Simulationen mit mehreren Auflösungsniveaus: ein Überblick über methodische Aspekte.
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- Angewandte Chemie, 2013, v. 125, n. 10, p. 2888, doi. 10.1002/ange.201205408
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- Article
Multi-Resolution Simulation of Biomolecular Systems: A Review of Methodological Issues.
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- Angewandte Chemie International Edition, 2013, v. 52, n. 10, p. 2820, doi. 10.1002/anie.201205408
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- Article
On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment.
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- Journal of Computational Chemistry, 2013, v. 34, n. 5, p. 387, doi. 10.1002/jcc.23146
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- Article
Conformational Preferences of a β-Octapeptide as Function of Solvent and Force-Field Parameters.
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- Helvetica Chimica Acta, 2013, v. 96, n. 2, p. 189, doi. 10.1002/hlca.201200173
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Die sieben Todsünden akademischen Handelns in der naturwissenschaftlichen Forschung.
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- Angewandte Chemie, 2013, v. 125, n. 1, p. 128, doi. 10.1002/ange.201204076
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The Seven Sins in Academic Behavior in the Natural Sciences.
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- Angewandte Chemie International Edition, 2013, v. 52, n. 1, p. 118, doi. 10.1002/anie.201204076
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Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code.
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- PLoS Genetics, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pgen.1003187
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Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12.
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- Protein Science: A Publication of the Protein Society, 2013, v. 22, n. 1, p. 56, doi. 10.1002/pro.2184
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- Article
Validation of the GROMOS 54A7 Force Field Regarding Mixed α/ β-Peptide Molecules.
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- Helvetica Chimica Acta, 2012, v. 95, n. 12, p. 2562, doi. 10.1002/hlca.201200534
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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.
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- Protein Science: A Publication of the Protein Society, 2012, v. 21, n. 11, p. 1672, doi. 10.1002/pro.2143
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Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages.
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- Journal of Computational Chemistry, 2012, v. 33, n. 26, p. 2108, doi. 10.1002/jcc.23047
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- Article
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.
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- Journal of Computational Chemistry, 2012, v. 33, n. 24, p. 1907, doi. 10.1002/jcc.23021
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- Article
Molecular dynamics simulation of thionated hen egg white lysozyme.
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- Protein Science: A Publication of the Protein Society, 2012, v. 21, n. 8, p. 1153, doi. 10.1002/pro.2102
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- Article
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9.
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- Journal of Computational Chemistry, 2012, v. 33, n. 17, p. 1467, doi. 10.1002/jcc.22972
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Temperature Dependence of the Dielectric Permittivity of Acetic Acid, Propionic Acid and Their Methyl Esters: A Molecular Dynamics Simulation Study.
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- ChemPhysChem, 2012, v. 13, n. 5, p. 1182, doi. 10.1002/cphc.201100949
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- Article
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution.
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- Journal of Computational Chemistry, 2012, v. 33, n. 6, p. 640, doi. 10.1002/jcc.22879
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On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations.
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- Journal of Computational Chemistry, 2012, v. 33, n. 4, p. 363, doi. 10.1002/jcc.21962
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New functionalities in the GROMOS biomolecular simulation software.
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- Journal of Computational Chemistry, 2012, v. 33, n. 3, p. 340, doi. 10.1002/jcc.21954
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- Article
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.
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- FEBS Journal, 2012, v. 279, n. 2, p. 299, doi. 10.1111/j.1742-4658.2011.08424.x
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- Article
Helical Content of a β<sup>3</sup>-Octapeptide in Methanol: Molecular Dynamics Simulations Explain a Seeming Discrepancy between Conclusions Derived from CD and NMR Data.
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- Chemistry - A European Journal, 2012, v. 18, n. 2, p. 586, doi. 10.1002/chem.201102667
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Preferential Affinity of the Components of Liquid Mixtures at a Rigid Non-Polar Surface: Enthalpic and Entropic Driving Forces.
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- ChemPhysChem, 2011, v. 12, n. 17, p. 3214, doi. 10.1002/cphc.201100541
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- Article
A Method for Conformational Sampling of Loops in Proteins Based on Adiabatic Decoupling and Temperature or Force Scaling.
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- ChemPhysChem, 2011, v. 12, n. 14, p. 2609, doi. 10.1002/cphc.201100305
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Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.
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- Journal of Computer-Aided Molecular Design, 2011, v. 25, n. 8, p. 709, doi. 10.1007/s10822-011-9453-x
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Conformational state-specific free energy differences by one-step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields.
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- Journal of Computational Chemistry, 2011, v. 32, n. 10, p. 2290, doi. 10.1002/jcc.21818
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Calculation of binding free energies of inhibitors to plasmepsin II.
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- Journal of Computational Chemistry, 2011, v. 32, n. 9, p. 1801, doi. 10.1002/jcc.21761
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- Article
Influence of Variation of a Side Chain on the Folding Equilibrium of a β-Peptide.
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- Helvetica Chimica Acta, 2011, v. 94, n. 4, p. 597, doi. 10.1002/hlca.201100003
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- Article
α-Cyclodextrin Host-Guest Binding: A Computational Study of the Different Driving Forces.
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- Helvetica Chimica Acta, 2010, v. 93, n. 12, p. 2318, doi. 10.1002/hlca.201000251
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Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements.
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- Protein Science: A Publication of the Protein Society, 2010, v. 19, n. 12, p. 2462, doi. 10.1002/pro.528
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A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability.
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- Protein Science: A Publication of the Protein Society, 2010, v. 19, n. 11, p. 2186, doi. 10.1002/pro.504
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- Article
Molecular Dynamics Simulation of Ester-Linked Hen Egg White Lysozyme Reveals the Effect of Missing Backbone Hydrogen Bond Donors on the Protein Structure.
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- Helvetica Chimica Acta, 2010, v. 93, n. 10, p. 1857, doi. 10.1002/hlca.201000077
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- Article
The Effect of Fluoro Substitution upon the β-Hairpin Fold of a β-Tetrapeptide in Methanol.
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- Helvetica Chimica Acta, 2010, v. 93, n. 10, p. 1870, doi. 10.1002/hlca.201000179
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Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a β-peptide in solution.
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- Journal of Computational Chemistry, 2010, v. 31, n. 13, p. 2419, doi. 10.1002/jcc.21534
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Basic ingredients of free energy calculations: A review.
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- Journal of Computational Chemistry, 2010, v. 31, n. 8, p. 1569, doi. 10.1002/jcc.21450
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A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.
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- Journal of Computational Chemistry, 2010, v. 31, n. 8, p. 1636, doi. 10.1002/jcc.21447
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What stabilizes the 3<sub>14</sub>-helix in β<sup>3</sup>-peptides? A conformational analysis using molecular simulation.
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- Proteins, 2010, v. 78, n. 7, p. 1677, doi. 10.1002/prot.22685
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- Article