(Q42106721)

16 October 2017

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

1 reference

16 October 2017

2

1 reference

16 October 2017

David L Mobley

1

0 references

Ken A. Dill

series ordinal

3

object named as

Ken A Dill

1 reference

PMCID

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

8

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

16 October 2017

1 reference

PMCID

3583553