The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change (Q30372513)

16 October 2017

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

1 reference

16 October 2017

3

Ken A Dill

1 reference

16 October 2017

David L Mobley

1

1 reference

PMC publication ID

2562444

16 October 2017

John D Chodera

series ordinal

2

1 reference

16 October 2017

1 January 2007

1 reference

Journal of Chemical Theory and Computation

16 October 2017

1 reference

16 October 2017

3

1 reference

16 October 2017

4

1 reference

16 October 2017

1231-1235

1 reference

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

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

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Direct calculation of the binding free energies of FKBP ligands

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

The many roles of computation in drug discovery

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

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

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

4 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Alchemical free energy calculations and multiple conformational substates

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Calculation of the Redox Potential of the Protein Azurin and Some Mutants

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2562444

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

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18843379

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT700032N

1 reference

16 October 2017

1 reference

PMC publication ID

2562444

16 October 2017

PubMed publication ID

18843379

1 reference

PMC publication ID

2562444