(Q36658081)

15 August 2017

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title

Comparison of free energy methods for molecular systems (English)

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15 August 2017

Daniel M Zuckerman

3

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Robert H. Swendsen

object named as

Robert H Swendsen

series ordinal

2

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author name string

F Marty Ytreberg

series ordinal

1

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15 August 2017

language of work or name

English

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publication date

1 November 2006

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Journal of Chemical Physics

15 August 2017

published in

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15 August 2017

volume

125

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15 August 2017

issue

18

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15 August 2017

page(s)

184114

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The many roles of computation in drug discovery

15 August 2017

cites work

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Ion solvation thermodynamics from simulation with a polarizable force field

21 January 2018

1 reference

Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment

21 January 2018

1 reference

Direct calculation of the binding free energies of FKBP ligands

21 January 2018

1 reference

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

21 January 2018

1 reference

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

21 January 2018

1 reference

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

21 January 2018

1 reference

Nonequilibrium Equality for Free Energy Differences

21 January 2018

1 reference

Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems.

21 January 2018

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Theory of a systematic computational error in free energy differences.

21 January 2018

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Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements

21 January 2018

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Phase-space overlap measures. II. Design and implementation of staging methods for free-energy calculations

21 January 2018

1 reference

Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation.

21 January 2018

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Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach

21 January 2018

1 reference

Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

21 January 2018

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Markov chains of infinite order and asymptotic satisfaction of balance: application to the adaptive integration method.

21 January 2018

1 reference

Using overlap and funnel sampling to obtain accurate free energies from nonequilibrium work measurements

21 January 2018

1 reference

Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics.

21 January 2018

1 reference

Computation of a chemical potential using a residence weight algorithm

21 January 2018

1 reference

Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation.

21 January 2018

1 reference

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

21 January 2018

1 reference

From transition paths to transition states and rate coefficients.

21 January 2018

1 reference

An efficient newton-like method for molecular mechanics energy minimization of large molecules

21 January 2018

1 reference

Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations

21 January 2018

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A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

21 January 2018

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

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

21 January 2018

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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

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Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens

21 January 2018

1 reference

Fast-growth thermodynamic integration: Error and efficiency analysis

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.2378907

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15 August 2017

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