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Literature DB >> 11143554

Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures.

Abstract

This article reviews measures for evaluating the effectiveness of similarity searches in chemical databases, drawing principally upon the many measures that have been described previously for evaluating the performance of text search engines. The use of the various measures is exemplified by fragment-based 2D similarity searches on several databases for which both structural and bioactivity data are available. It is concluded that the cumulative recall and G-H score measures are the most useful of those tested.

Mesh：

Year: 2000 PMID： 11143554 DOI： 10.1016/s1093-3263(00)00061-9

Source DB: PubMed Journal: J Mol Graph Model ISSN： 1093-3263 Impact factor: 2.518

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Cited

11 in total

1. Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases.

Authors: John W Raymond; Peter Willett
Journal: J Comput Aided Mol Des Date: 2002-01 Impact factor: 3.686

Review 2. Molecular similarity and diversity in chemoinformatics: from theory to applications.

Authors: Ana G Maldonado; J P Doucet; Michel Petitjean; Bo-Tao Fan
Journal: Mol Divers Date: 2006-02 Impact factor: 2.943

Review 3. A cheminformatic toolkit for mining biomedical knowledge.

Authors: Gus R Rosania; Gordon Crippen; Peter Woolf; David States; Kerby Shedden
Journal: Pharm Res Date: 2007-03-24 Impact factor: 4.200

4. Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results.

Authors: Robert P Sheridan; Georgia B McGaughey; Wendy D Cornell
Journal: J Comput Aided Mol Des Date: 2008-02-14 Impact factor: 3.686

5. Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios.

Authors: Dimitar P Hristozov; Tudor I Oprea; Johann Gasteiger
Journal: J Comput Aided Mol Des Date: 2007-11-16 Impact factor: 3.686

Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures.

1. Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases.

Review 2. Molecular similarity and diversity in chemoinformatics: from theory to applications.

Review 3. A cheminformatic toolkit for mining biomedical knowledge.

4. Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results.

5. Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios.

6. Application of 3D Zernike descriptors to shape-based ligand similarity searching.

7. Evaluation of a Bayesian inference network for ligand-based virtual screening.

8. Virtual screening by a new Clustering-based Weighted Similarity Extreme Learning Machine approach.

9. Predictiveness curves in virtual screening.

10. Target enhanced 2D similarity search by using explicit biological activity annotations and profiles.