(Q51608662)

English

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.

scientific article published on 31 December 2010

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method. (English)

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

2

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

author name string

Stefan Bruckner

1

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

publication date

31 December 2010

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

Journal of Computational Chemistry

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

32

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

7

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

1303-1319

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Calculation of absolute protein-ligand binding free energy from computer simulations

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Predicting absolute ligand binding free energies to a simple model site

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity.

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Nonequilibrium Equality for Free Energy Differences

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Theory of a systematic computational error in free energy differences.

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Asymmetric bias in free-energy perturbation measurements using two Hamiltonian-based models.

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Model for small-sample bias of free-energy calculations applied to Gaussian-distributed nonequilibrium work measurements.

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Comparison of free energy methods for molecular systems

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Assessment of nonequilibrium free energy methods

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Good practices in free-energy calculations

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Direct calculation of the binding free energies of FKBP ligands

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Statistically optimal analysis of samples from multiple equilibrium states

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Alchemical free energy calculations and multiple conformational substates

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Free energy via molecular simulation: applications to chemical and biomolecular systems

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

CHARMM: the biomolecular simulation program

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Comparison of simple potential functions for simulating liquid water

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Hydration free energies of amino acids: why side chain analog data are not enough

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Structure of protein tyrosine phosphatase 1B in complex with inhibitors bearing two phosphotyrosine mimetics

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

The difluoromethylenesulfonic acid group as a monoanionic phosphate surrogate for obtaining PTP1B inhibitors

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Unexpected relative aqueous solubilities of a phosphotyrosine analogue and two phosphonate derivatives

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Canonical dynamics: Equilibrium phase-space distributions

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Gaussian fluctuations and linear response in an electron transfer protein

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface.

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Convergence Properties of Free Energy Calculations: .alpha.-Cyclodextrin Complexes as a Case Study

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Unorthodox uses of Bennett's acceptance ratio method

1 reference

https://api.crossref.org/works/10.1002%2FJCC.21713

21 January 2018

Identifiers

10.1002/JCC.21713

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

DBLP publication ID

journals/jcc/BrucknerB11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

8 April 2018

http://europepmc.org/abstract/MED/21425288

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q51608662&oldid=1360125898"