sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets

sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create his/her own database by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data, and (4) building the classification model of biological activity.

sMOL Explorer has been developed as a collection of Java Server Pages (JSP) and Servlets running on the Apache Tomcat web server, utilizing MySQL database management and several chemical informatics libraries such as CDK, JOELib, and Open Babel for data manipulation, and connecting to various data analysis and mining methods from the Weka library and R statistical environment. After the installation, only a web browser is needed for using sMOL Explorer.

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