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PROTEUS- Protein databank (PDB) file representation for Structural analysis

IP.com Disclosure Number: IPCOM000010789D
Original Publication Date: 2003-Jan-22
Included in the Prior Art Database: 2003-Jan-22
Document File: 5 page(s) / 42K

Publishing Venue

IBM

Abstract

The Human Genome Project, in its "Quest for the Holy Grail", has thrown up several challenges and interesting revelations in its wake. One of the outstanding and fundamental revelations has been the revision of the central dogma of genetics... While earlier geneticists believed that nature worked along the lines of DNA-->RNA-->Protein, present day genetics has given rise and lent credence to the new dogma, i.e. Sequence-->Structure-->Function. This has opened up relatively new avenues in genetics like "Structural Genomics". Structural genomics involves the determination, analysis, and dissemination of the three-dimensional structures of all protein and RNA molecules in nature, providing new opportunities at the interface of structural biology, functional genomics, and bioinformatics. All the experimentally determined structural information of the proteins is stored in PDB file formats The PDB was established in 1971 with a handful of structures at Brookhaven National Laboratory. Revisions and modifications are now handled by the RCSB consortium (www.rcsb.org). The PDB files form the foundation for any structural processing and analysis; be it three-dimensional structure rendering, structure comparison etc. And it is imperative that this file be parsed every time it has to be used. The PDB file is fairly complicated with a lot of connectivity information between various atoms in the amino acid encoded in specific fields. With Genome scale structural analysis likely to assume critical importance in future, it is absolutely essential that PDB files are represented in a format that is more amenable to tools that may be used for structure rendering, analysis etc. PROTEUS is a radically simple data structure that holds all the amino acid information and the atom connectivity information. In addition, it has an associated set of algorithms that convert the information from the PDB files into PROTEUS.