OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation - Wikidata - wikimedia - TriplyDB

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

http://www.wikidata.org/entity/Q30415382

about

MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery Markov state models of biomolecular conformational dynamics Markov state models provide insights into dynamic modulation of protein function Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive Chromatin loops as allosteric modulators of enhancer-promoter interactions Ubiquinone-binding site mutagenesis reveals the role of mitochondrial complex II in cell death initiation Open source molecular modeling Blinded predictions of distribution coefficients in the SAMPL5 challenge An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications pH-dependent transient conformational states control optical properties in cyan fluorescent protein A Simple Method for Automated Equilibration Detection in Molecular Simulations.Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units Internal coordinate molecular dynamics: a foundation for multiscale dynamics Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models.Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference A network of molecular switches controls the activation of the two-component response regulator NtrC.Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations Blind protein structure prediction using accelerated free-energy simulations Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter.Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems.Compaction and segregation of sister chromatids via active loop extrusion.Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank.Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa.GneimoSim: a modular internal coordinates molecular dynamics simulation package.Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design.MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.United polarizable multipole water model for molecular mechanics simulation Equilibrium molecular thermodynamics from Kirkwood sampling.Current status of protein force fields for molecular dynamics simulations.Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale WESTPA: an interoperable, highly scalable software package for weighted ensemble simulation and analysis Accelerating molecular simulations of proteins using Bayesian inference on weak information.Modeling molecular kinetics with tICA and the kernel trick Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model The DDR at telomeres lacking intact shelterin does not require substantial chromatin decompaction.

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OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

http://www.wikidata.org/entity/Q30415382

description

2012 nî lūn-bûn

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2012 թուականի Հոկտեմբերին հրատարակուած գիտական յօդուած

@hyw

2012 թվականի հոտեմբերին հրատարակված գիտական հոդված

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2012年の論文

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2012年論文

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2012年論文

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2012年論文

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2012年論文

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2012年論文

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2012年论文

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name

OpenMM 4: A Reusable, Extensib ...... rformance Molecular Simulation

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OpenMM 4: A Reusable, Extensib ...... rformance Molecular Simulation

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OpenMM 4: A Reusable, Extensib ...... rformance Molecular Simulation

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OpenMM 4: A Reusable, Extensib ...... rformance Molecular Simulation

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P1433

Journal of Chemical Theory and Computation

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OpenMM 4: A Reusable, Extensib ...... rformance Molecular Simulation

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P2093

Christoph Klein

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Christopher M Bruns

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Diwakar Shukla

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John D Chodera

http://www.w3.org/2001/XMLSchema#string

Joy P Ku

http://www.w3.org/2001/XMLSchema#string

Kyle A Beauchamp

http://www.w3.org/2001/XMLSchema#string

Mark S Friedrichs

http://www.w3.org/2001/XMLSchema#string

Mike Houston

http://www.w3.org/2001/XMLSchema#string

Peter Eastman

http://www.w3.org/2001/XMLSchema#string

Randall J Radmer

http://www.w3.org/2001/XMLSchema#string

P2860

Accelerating molecular dynamic simulation on graphics processing units

CHARMM: the biomolecular simulation program

Structure of ubiquitin refined at 1.8 A resolution

Scalable molecular dynamics with NAMD

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Exploring protein native states and large-scale conformational changes with a modified generalized born model

Statistically optimal analysis of samples from multiple equilibrium states.

Identifying low variance pathways for free energy calculations of molecular transformations in solution phase.

A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods.

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461-469

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scholarly article

P356

10.1021/CT300857J

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P433

1

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P478

9

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P50

Michael R Shirts

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2012-10-18T00:00:00Z

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234124976

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23316124

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open source hardware

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3539733

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