about
Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials.Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials.Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting.Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions.Identifying Differences and Similarities in Static and Dynamic Contact Angles between Nanoscale and Microscale Textured Surfaces Using Molecular Dynamics Simulations.Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study.Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular SimulationProduct binding varies dramatically between processive and nonprocessive cellulase enzymes.Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures.Alchemical free energy methods for drug discovery: progress and challengesProbing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods.Statistically optimal analysis of samples from multiple equilibrium states.Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange.Best practices in free energy calculations for drug design.Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase.An introduction to best practices in free energy calculations.Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude.Investigating the mutation resistance of nonnucleoside inhibitors of HIV-RT using multiple microsecond atomistic simulations.Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations.Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations.Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites.Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations.Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles.A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods.Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing.Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing.Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration.Accurate and efficient corrections for missing dispersion interactions in molecular simulations.Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy.Overview of the SAMPL5 host-guest challenge: Are we doing better?Native-like mean structure in the unfolded ensemble of small proteins.Direct calculation of the binding free energies of FKBP ligands.Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations.Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations.
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onderzoeker
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researcher
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հետազոտող
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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Michael R Shirts
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P31
P496
0000-0003-3249-1097