(Q35921319)

11 August 2017

Theory of binless multi-state free energy estimation with applications to protein-ligand binding (English)

1 reference

11 August 2017

1 reference

Emilio Gallicchio

2

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author name string

Zhiqiang Tan

series ordinal

1

1 reference

11 August 2017

Mauro Lapelosa

series ordinal

3

1 reference

11 August 2017

Ronald M Levy

series ordinal

4

1 reference

11 August 2017

language of work or name

English

0 references

publication date

1 April 2012

1 reference

Journal of Chemical Physics

11 August 2017

1 reference

11 August 2017

136

1 reference

11 August 2017

14

1 reference

11 August 2017

144102

1 reference

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

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Recent theoretical and computational advances for modeling protein-ligand binding affinities

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Alchemical free energy methods for drug discovery: progress and challenges

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Advances in all atom sampling methods for modeling protein-ligand binding affinities

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Basic ingredients of free energy calculations: a review

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Computations of standard binding free energies with molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Statistically optimal analysis of samples from multiple equilibrium states

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Direct calculation of the binding free energies of FKBP ligands

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Good practices in free-energy calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

Temperature weighted histogram analysis method, replica exchange, and transition paths.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3339880

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

24 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.3701175

A theory of statistical models for Monte Carlo integration

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1063%2F1.3701175

Linear-scaling soft-core scheme for alchemical free energy calculations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22502496

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Optimized Monte Carlo data analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22502496

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.3701175

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22502496

1 reference