(Q28391043)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration (English)

1 reference

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1 March 2020

9

1 reference

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1 March 2020

8

Celia A Schiffer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

author name string

Nathaniel W Silver

1

1 reference

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1 March 2020

Bracken M King

2

1 reference

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1 March 2020

Madhavi N L Nalam

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Hong Cao

4

1 reference

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1 March 2020

Akbar Ali

5

1 reference

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1 March 2020

G S Kiran Kumar Reddy

6

1 reference

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1 March 2020

Tariq M Rana

7

1 reference

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1 March 2020

language of work or name

English

0 references

publication date

7 August 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

1 March 2020

published in

1 reference

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1 March 2020

volume

9

1 reference

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1 March 2020

issue

11

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1 March 2020

page(s)

5098-5115

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

Thermodynamic and differential entropy under a change of variables

1 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Efficient calculation of molecular configurational entropies using an information theoretic approximation

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed To Be Robust against Drug Resistance

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Theory of free energy and entropy in noncovalent binding

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

CHARMM: the biomolecular simulation program

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

The Amber biomolecular simulation programs

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Rotamer libraries in the 21st century

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

20 March 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

De novo protein design: fully automated sequence selection

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Novel fluorogenic substrates for assaying retroviral proteases by resonance energy transfer

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Extraction of configurational entropy from molecular simulations via an expansion approximation

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

A Statistical Framework for Hierarchical Methods in Molecular Simulation and Design

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

The dead-end elimination theorem and its use in protein side-chain positioning

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Targeting structural flexibility in HIV-1 protease inhibitor binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Ligand configurational entropy and protein binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

On the calculation of absolute macromolecular binding free energies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Protein design automation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Empirical scale of side-chain conformational entropy in protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Free energy via molecular simulation: applications to chemical and biomolecular systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Evaluation of methods for estimating the dissociation constant of tight binding enzyme inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Evaluating the Accuracy of the Quasiharmonic Approximation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Maximum entropy formulation of the Kirkwood superposition approximation.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Novel scoring functions comprising QXP, SASA, and protein side-chain entropy terms.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Contributions to the binding free energy of ligands to avidin and streptavidin.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3827837

Calculations of solute and solvent entropies from molecular dynamics simulations

27 November 2018

1 reference

12 December 2020

Tautomers and topomers: challenging the uncertainties of direct physicochemical modeling

1 reference

12 December 2020

Absolute and relative entropies from computer simulation with applications to ligand binding

1 reference

12 December 2020

Physical nature of higher-order mutual information: intrinsic correlations and frustration

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT400383V

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24250277%20AND%20SRC:MED&resulttype=core&format=json