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Bioinformatics Advance Access published online on July 27, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm363
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Supawadee Ingsriswang * and Eakasit Pacharawongsakda

Information Systems Laboratory, BIOTEC Central Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Klongluang, Pathumthani, 12120, Thailand.

*To whom correspondence should be addressed. Supawadee Ingsriswang, E-mail: supawadee{at}biotec.or.th


  Abstract

Summary: 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 ownpersonal databases 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 from Weka and R packages 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.

Availability: sMOL Explorer is an Open Source project and is freely available to all interested users at http://www.biotec.or.th/ISL/SMOL/.

Contact: supawadee{at}biotec.or.th

Associate Editor: Dr. Limsoon Wong

Received on June 26, 2007; revised on July 9, 2007; accepted on July 9, 2007

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