(Q47948501)

7 February 2018

title

Massively parallel computation of absolute binding free energy with well-equilibrated states (English)

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7 February 2018

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Hideaki Fujitani

1

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7 February 2018

Yoshiaki Tanida

series ordinal

2

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7 February 2018

Azuma Matsuura

series ordinal

3

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7 February 2018

language of work or name

English

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publication date

26 February 2009

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7 February 2018

published in

Physical Review E

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7 February 2018

volume

79

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7 February 2018

issue

2 Pt 1

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7 February 2018

page(s)

021914

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7 February 2018

Nonequilibrium Equality for Free Energy Differences

cites work

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Direct calculation of the binding free energies of FKBP ligands

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Development and testing of a general amber force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Automatic atom type and bond type perception in molecular mechanical calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

GROMACS: fast, flexible, and free

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

The Amber biomolecular simulation programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Calculating potentials of mean force from steered molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Statistical mechanical derivation of Jarzynski's identity for thermostated non-Hamiltonian dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

A common, avoidable source of error in molecular dynamics integrators.

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Canonical dynamics: Equilibrium phase-space distributions

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

VMD: visual molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

Fast-growth thermodynamic integration: Error and efficiency analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1103%2FPHYSREVE.79.021914

10.1103/PHYSREVE.79.021914

21 January 2018

Identifiers

DOI

1 reference

7 February 2018

release_qgubsmbph5fmdfc6o266y3hna4

ADS bibcode

2009PhRvE..79b1914F

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Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/qgubsmbph5fmdfc6o266y3hna4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

7 February 2018