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Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsinGROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationGROMACS: fast, flexible, and freeGROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.Fluorescence probe of Trp-cage protein conformation in solution and in gas phase.Structural stability of electrosprayed proteins: temperature and hydration effects.Proteins, lipids, and water in the gas phase.An efficient and extensible format, library, and API for binary trajectory data from molecular simulations.Molecular dynamics simulations of peptides from the central domain of smooth muscle caldesmon.Deciphering solution scattering data with experimentally guided molecular dynamics simulations.Water Determines the Structure and Dynamics of Proteins.A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors.Model for the dynamics of a water cluster in an x-ray free electron laser beam.Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media.Protein structures under electrospray conditions.Structural studies of melting on the picosecond time scale.Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP).Structural variability and the incoherent addition of scattered intensities in single-particle diffraction.Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data.GROMACS molecule & liquid database.Virus capsid dissolution studied by microsecond molecular dynamics simulations.Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.Speeding up parallel GROMACS on high-latency networks.Time-resolved WAXS reveals accelerated conformational changes in iodoretinal-substituted proteorhodopsin.Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.Impact of sludge deposition on biodiversity.Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models.Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations.Thiamin function, metabolism, uptake, and transport.Chemical properties, environmental fate, and degradation of seven classes of pollutants.Efficient docking of peptides to proteins without prior knowledge of the binding site.Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents.Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes.Binding of Pollutants to Biomolecules: A Simulation Study.Exploration of Interfacial Hydration Networks of Target-Ligand Complexes.Blind docking of drug-sized compounds to proteins with up to a thousand residues.Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.Local partition coefficients govern solute permeability of cholesterol-containing membranes.Toward prediction of functional protein pockets using blind docking and pocket search algorithms.
P50
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P50
description
hulumtues
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researcher
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հետազոտող
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name
David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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type
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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D. van der Spoel
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D. van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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David van der Spoel
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P1053
A-5471-2008
P106
P1960
tTsoeUoAAAAJ
P21
P31
P3829
P496
0000-0002-7659-8526