Ligand configurational entropy and protein binding (Q35607011)

9 August 2017

title

Ligand configurational entropy and protein binding (English)

1 reference

9 August 2017

Chia-en A Chang

1

1 reference

9 August 2017

Wei Chen

series ordinal

2

1 reference

9 August 2017

Michael K Gilson

series ordinal

3

1 reference

9 August 2017

language of work or name

English

0 references

publication date

22 January 2007

1 reference

Proceedings of the National Academy of Sciences of the United States of America

9 August 2017

published in

1 reference

9 August 2017

volume

104

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9 August 2017

issue

5

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9 August 2017

page(s)

1534-1539

1 reference

Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations

9 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Ligand efficiency: a useful metric for lead selection

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Binding Affinities of Host–Guest, Protein–Ligand, and Protein–Transition‐State Complexes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

On the calculation of absolute macromolecular binding free energies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

12 July 2018

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=1780070

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Side-chain conformational entropy in protein folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Empirical scale of side-chain conformational entropy in protein folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Decomposition of interaction free energies in proteins and other complex systems.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Configurational entropy of native proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

The Protein Data Bank: a computer-based archival file for macromolecular structures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Concepts in receptor optimization: targeting the RGD peptide.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Direct estimation of entropy loss due to reduced translational and rotational motions upon molecular binding

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Identification of symmetries in molecules and complexes.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Tork: Conformational analysis method for molecules and complexes

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Ligand-receptor docking with the Mining Minima optimizer.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

A fast flexible docking method using an incremental construction algorithm.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Evaluating the Accuracy of the Quasiharmonic Approximation

25 September 2018

1 reference

Crossref

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Entropy calculations on the molten globule state of a protein: Side-chain entropies of α-lactalbumin

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1780070

Thermodynamic characteristics for the formation of H-bonded DNA base pairs

23 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0610494104

Thermodynamics of the hydrophobic effect. III. Condensation and aggregation of alkanes, alcohols, and alkylamines

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17242351

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The price of lost freedom: entropy of bimolecular complex formation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17242351

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0610494104

1 reference

9 August 2017

0 references

1 reference

9 August 2017

1 reference