ChemmineR: a compound mining framework for R

Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popularstatistical programming environment R. The integrati...

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Bibliographic Details
Published in:Bioinformatics 2008-08, Vol.24 (15), p.1733-1734
Main Authors: Cao, Yiqun, Charisi, Anna, Cheng, Li-Chang, Jiang, Tao, Girke, Thomas
Format: Article
Language:English
Subjects:
Algorithms
Applications Note
Biological and medical sciences
Biopolymers - chemistry
Database Management Systems
Databases, Factual
Fundamental and applied biological sciences. Psychology
General aspects
Information Storage and Retrieval - methods
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Programming Languages
Software
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Summary:Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popularstatistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions. Results: We discuss the algorithms and compound mining utilities provided by the R package ChemmineR. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is well integrated with the online ChemMine environment and allows bidirectional communications between the two services. Availability: ChemmineR is freely available as an R package from the ChemMine project site: http://bioweb.ucr.edu/ChemMineV2/chemminer Contact: thomas.girke@ucr.edu
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btn307