(Q24683618)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

title

Predicting absolute ligand binding free energies to a simple model site (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

6

Ken A Dill

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

author name string

Alan P Graves

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

John D Chodera

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

Andrea C McReynolds

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

Brian K Shoichet

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

language of work or name

English

0 references

publication date

8 June 2007

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

number of pages

17

1 reference

Journal of Molecular Biology

inferred from page(s)

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

volume

371

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

page(s)

1118-1134

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

A model binding site for testing scoring functions in molecular docking

1 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

GROMACS: fast, flexible, and free

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Coot: model-building tools for molecular graphics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Refinement of macromolecular structures by the maximum-likelihood method

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Principles of docking: An overview of search algorithms and a guide to scoring functions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Development and testing of a general amber force field

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Automatic atom type and bond type perception in molecular mechanical calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Accurate and efficient corrections for missing dispersion interactions in molecular simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Molecular mechanics methods for predicting protein-ligand binding.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Direct calculation of the binding free energies of FKBP ligands

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Enhancing the accuracy, the efficiency and the scope of free energy simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Testing a flexible-receptor docking algorithm in a model binding site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Second-site revertants of an inactive T4 lysozyme mutant restore activity by restructuring the active site cleft

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

A new ultrasensitive scanning calorimeter.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

On the value of c: can low affinity systems be studied by isothermal titration calorimetry?

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Ligand solvation in molecular docking.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2104542

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

28 November 2018

1 reference

12 December 2020

A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase

1 reference

12 December 2020

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

1 reference

12 December 2020

Processing of X-ray diffraction data collected in oscillation mode

1 reference

12 December 2020

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

1 reference

12 December 2020

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

12 December 2020

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2007.06.002

7 January 2021

GROMACS 3.0: a package for molecular simulation and trajectory analysis

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2007.06.002

7 January 2021

Absolute Binding Free Energies: A Quantitative Approach for Their Calculation

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2007.06.002

7 January 2021

Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2007.06.002

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2007.06.002

7 January 2021

Molecular dynamics with coupling to an external bath

1 reference

https://api.crossref.org/works/10.1016%2FJ.JMB.2007.06.002

7 January 2021

10.1016/J.JMB.2007.06.002

Identifiers

DOI

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17599350%20AND%20SRC:MED&resulttype=core&format=json

1 January 2020

2 references