Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds

Proteins
M D PrasannaT N Bhat

Abstract

A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease-inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These standard fragments are defined by using criteria, such as chemical classification; structural, chemical, or functional groups; and commercial, scientific or common names or synonyms. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree to enable query on inhibitors of HIV protease (http://xpdb.nist.gov/hivsdb/hivsdb.html). These search engines use a new novel technique, Chemical Block Layered Alignment of Substructure Technique (Chem-BLAST) to search on the fragments of an inhibitor to look for its chemical structural neighbors. This novel technique to annotate and query compounds lays the foundation for the use of the Semantic Web concept on chemical compounds to allow end users to group, sort, and search structural neighbors accurately and efficiently. During annotation, it enables the attachment of "meaning" (i.e., semantics) to data in a manner that far...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 1, 1994·Annual Review of Biophysics and Biomolecular Structure·P J Whittle, T L Blundell
Jan 1, 1993·Annual Review of Biochemistry·A Wlodawer, J W Erickson
Jan 1, 1995·Advances in Experimental Medicine and Biology·T N BhatJ W Erickson
Jul 19, 1996·Journal of Medicinal Chemistry·G W Bemis, M A Murcko
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Dec 22, 1999·Pharmacology & Therapeutics·D Joseph-McCarthy
Mar 17, 2000·Science·J Drews
Dec 5, 2000·Nature Structural Biology·H M BermanJ Westbrook
Jan 11, 2000·Nucleic Acids Research·T N BhatH M Berman
Dec 26, 2001·Nucleic Acids Research·John WestbrookHelen M Berman
May 25, 2002·Nature·David Adam
Oct 29, 2002·Proteins·Jiri Vondrasek, Alexander Wlodawer
Jan 10, 2003·Nucleic Acids Research·Dennis A BensonDavid L Wheeler
Jan 10, 2003·Nucleic Acids Research·Brigitte BoeckmannMichel Schneider
Apr 30, 2005·Proteins·M D PrasannaT N Bhat

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Citations

Dec 23, 2011·BMC Bioinformatics·Anne L PlantTalapady N Bhat
Jan 10, 2012·BMC Bioinformatics·Leonid L ChepelevMichel Dumontier
Jan 1, 2013·Journal of Cheminformatics·Claudia BobachLutz Weber
Jun 8, 2011·Journal of Computational Chemistry·Elisabet Gregori-PuigjanéJordi Mestres
Jun 18, 2015·Journal of Computer-aided Molecular Design·Wendy A Warr
Jun 29, 2016·Journal of Biomedical Informatics·Rama Kaalia, Indira Ghosh
Apr 14, 2009·Journal of Chemical Theory and Computation·Adrian P WileyJonathan W Essex

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