Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. (Q37412834)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19736924%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

title

Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction (English)

1 reference

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7 February 2020

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5

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7 February 2020

author name string

Chao-Yie Yang

1

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7 February 2020

Haiying Sun

2

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7 February 2020

Jianyong Chen

3

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7 February 2020

Zaneta Nikolovska-Coleska

4

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7 February 2020

language of work or name

English

0 references

publication date

1 September 2009

1 reference

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Journal of the American Chemical Society

7 February 2020

published in

1 reference

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7 February 2020

volume

131

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7 February 2020

issue

38

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7 February 2020

page(s)

13709-13721

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Orally bioavailable antagonists of inhibitor of apoptosis proteins based on an azabicyclooctane scaffold

7 February 2020

cites work

1 reference

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Design, synthesis, and evaluation of potent, nonpeptidic mimetics of second mitochondria-derived activator of caspases

6 September 2017

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Potent, orally bioavailable diazabicyclic small-molecule mimetics of second mitochondria-derived activator of caspases

6 September 2017

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Design, synthesis, and evaluation of tricyclic, conformationally constrained small-molecule mimetics of second mitochondria-derived activator of caspases

6 September 2017

1 reference

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Structure-Based Design, Synthesis, Evaluation, and Crystallographic Studies of Conformationally Constrained Smac Mimetics as Inhibitors of the X-linked Inhibitor of Apoptosis Protein (XIAP) †

6 September 2017

1 reference

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Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

6 September 2017

1 reference

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Design, synthesis, and characterization of a potent, nonpeptide, cell-permeable, bivalent Smac mimetic that concurrently targets both the BIR2 and BIR3 domains in XIAP

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Calculation of protein-ligand binding affinities.

6 September 2017

1 reference

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Design, synthesis, and biological activity of a potent Smac mimetic that sensitizes cancer cells to apoptosis by antagonizing IAPs

6 September 2017

1 reference

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Targeting mitochondrial factor Smac/DIABLO as therapy for multiple myeloma (MM)

6 September 2017

1 reference

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A critical assessment of docking programs and scoring functions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Structural basis of IAP recognition by Smac/DIABLO

6 September 2017

1 reference

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Structural basis for binding of Smac/DIABLO to the XIAP BIR3 domain

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Generalized born models of macromolecular solvation effects

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

6 September 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=2773700

Development and validation of a genetic algorithm for flexible docking

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

M-score: a knowledge-based potential scoring function accounting for protein atom mobility.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Structure-based design, synthesis and biochemical testing of novel and potent Smac peptido-mimetics.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Comparative evaluation of 11 scoring functions for molecular docking

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Knowledge-based scoring function to predict protein-ligand interactions.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2773700

Structure-based design of potent, conformationally constrained Smac mimetics

2 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19736924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Non-peptidic small molecule inhibitors of XIAP

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19736924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JA9039373

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19736924%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19736924%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

1 reference