On the use of orientational restraints and symmetry corrections in alchemical free energy calculations (Q42106721)

16 October 2017

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

1 reference

16 October 2017

1 reference

16 October 2017

David L Mobley

0 references

Ken A Dill

1 reference

PMC publication ID

3583553

16 October 2017

language of work or name

English

0 references

publication date

1 August 2006

1 reference

Journal of Chemical Physics

16 October 2017

1 reference

16 October 2017

125

1 reference

16 October 2017

1 reference

16 October 2017

084902

1 reference

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

16 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

GROMACS: fast, flexible, and free

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Direct calculation of the binding free energies of FKBP ligands

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Docking and scoring in virtual screening for drug discovery: methods and applications

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Development and testing of a general amber force field

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

A model binding site for testing scoring functions in molecular docking

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Thermodynamics of buried water clusters at a protein-ligand binding interface

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

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

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Alchemical free energy calculations and multiple conformational substates

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3583553

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

17 August 2018

1 reference

Inference from Iterative Simulation Using Multiple Sequences

21 January 2018

1 reference

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

Ligand solvation in molecular docking.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions

21 January 2018

1 reference

On the limited memory BFGS method for large scale optimization

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16965052

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16965052

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.2221683

1 reference

16 October 2017

1 reference

PMC publication ID

3583553

16 October 2017

PubMed publication ID

16965052

1 reference

PMC publication ID

3583553