(Q84395800)

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Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors

scientific article published on 16 June 2012

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Europe PubMed Central

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5 February 2020

Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors (English)

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Europe PubMed Central

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5 February 2020

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Mahmoud A Al-Sha'er

1

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5 February 2020

Mutasem O. Taha

2

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5 February 2020

publication date

16 June 2012

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5 February 2020

Journal of Molecular Modeling

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5 February 2020

18

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5 February 2020

11

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5 February 2020

4843-4863

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5 February 2020

A fluorescence polarization assay for inhibitors of Hsp90.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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Hydration in drug design. 2. Influence of local site surface shape on water binding

1 reference

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12 December 2020

based on heuristic

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Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?

1 reference

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12 December 2020

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Development of a purine-scaffold novel class of Hsp90 binders that inhibit the proliferation of cancer cells and induce the degradation of Her2 tyrosine kinase

1 reference

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12 December 2020

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Scoring functions: a view from the bench

1 reference

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Using natural product inhibitors to validate Hsp90 as a molecular target in cancer

1 reference

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

1 reference

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Discovery of potent inhibitors of pseudomonal quorum sensing via pharmacophore modeling and in silico screening.

1 reference

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Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

1 reference

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12 December 2020

based on heuristic

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Emerging Hsp90 inhibitors: from discovery to clinic

1 reference

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Development of Radicicol Analogues

1 reference

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12 December 2020

based on heuristic

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Discovery and development of purine-scaffold Hsp90 inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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A novel class of Hsp90 inhibitors isolated by structure-based virtual screening

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Homology modeling of MCH1 receptor and validation by docking/scoring and protein-aligned CoMFA.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Virtual screening using protein-ligand docking: avoiding artificial enrichment.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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ZINC--a free database of commercially available compounds for virtual screening

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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Lead- and drug-like compounds: the rule-of-five revolution

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Effects of variable docking conditions and scoring functions on corresponding protein-aligned comparative molecular field analysis models constructed from diverse human protein tyrosine phosphatase 1B inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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PMF scoring revisited

1 reference

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12 December 2020

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Geldanamycin as a potential anti-cancer agent: its molecular target and biochemical activity

1 reference

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12 December 2020

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Discovery and development of pyrazole-scaffold Hsp90 inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Development and validation of a genetic algorithm for flexible docking

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Discovery and design of novel HSP90 inhibitors using multiple fragment-based design strategies

1 reference

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12 December 2020

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Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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Discovery of benzisoxazoles as potent inhibitors of chaperone heat shock protein 90

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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A Strategy for the Incorporation of Water Molecules Present in a Ligand Binding Site into a Three-Dimensional Quantitative Structure−Activity Relationship Analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Scoring functions for protein-ligand docking

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Towards accurate free energy calculations in ligand protein-binding studies

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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An improved assay for nanomole amounts of inorganic phosphate

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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Efficient drug lead discovery and optimization

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The complex dance of the molecular chaperone Hsp90.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

High-throughput screening for Hsp90 ATPase inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

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inferred from PubMed ID database lookup

Impact of scoring functions on enrichment in docking-based virtual screening: an application study on renin inhibitors.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Combining docking, scoring and molecular field analyses to probe influenza neuraminidase–ligand interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Some sulfonamide drugs inhibit ATPase activity of heat shock protein 90: investigation by docking simulation and experimental validation.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Heat shock protein 90 as a molecular target for cancer therapeutics

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effectiveness of hsp90 inhibitors as anti-cancer drugs

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Virtual Screening with AutoDock: Theory and Practice

1 reference

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12 December 2020

based on heuristic

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Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Water, water everywhere--except where it matters?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluation of docking performance: comparative data on docking algorithms

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

4-Amino derivatives of the Hsp90 inhibitor CCT018159.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Tackling the challenges posed by target flexibility in drug design

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Improving structure-based virtual screening by multivariate analysis of scoring data

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Towards predictive ligand design with free-energy based computational methods?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Recent advances in computer-aided drug design

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Development and optimization of a useful assay for determining Hsp90's inherent ATPase activity

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A fast flexible docking method using an incremental construction algorithm.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Hsp90 molecular chaperone: an open and shut case for treatment

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

High throughput docking for library design and library prioritization

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Targeting HSP90 for cancer therapy

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Virtual ligand screening: strategies, perspectives and limitations

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

4,5-diarylisoxazole Hsp90 chaperone inhibitors: potential therapeutic agents for the treatment of cancer

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

LigScore: a novel scoring function for predicting binding affinities

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative evaluation of 11 scoring functions for molecular docking

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Elaborate ligand-based modeling reveals new nanomolar heat shock protein 90α inhibitors.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structure-based discovery of a new class of Hsp90 inhibitors

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal contacts as nature's docking solutions

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Discovery of DPP IV inhibitors by pharmacophore modeling and QSAR analysis followed by in silico screening.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22707278

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1007/S00894-012-1479-Z

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22707278%20AND%20SRC:MED&resulttype=core&format=json

5 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22707278%20AND%20SRC:MED&resulttype=core&format=json

5 February 2020

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