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Title: Incorporating Sequence and Biochemical Information in Topological Models of Protein Structure Towards the Structural and Functional Genomics
P169
Veeramalai, Mallika (1); Gilbert, David (1); Westhead, David (2)

mallika@brc.dcs.gla.ac.uk, drg@brc.dcs.gla.ac.uk, westhead@bioinformatics.leeds.ac.uk
University of Glasgow(1), University of Leeds(2)

TOPS (Topology of Protein Structure) Database contains 2D abstract cartoon representation of the protein structure (Westhead et.al., 1999). For example following figure:1 shows the TOPS cartoon for 2bopA0 DNA binding protein with the secondary structure elements (SSEs), here circles indicates the alpha-helices and triangles indicates the beta-strands and the sequential order of the SSEs are described by the joining lines starting from N-terminal (N1) and ending with C-terminal (C2). Based on these TOPS cartoons TOPS diagrams are developed by (Gilbert et.al.,1999). Instead of representing spatial positions by elements in a plane, a TOPS diagram contains information about the grouping of beta-strands in beta-sheets (two adjacent elements in a beta-sheet are connected by an H-bond, which can be either parallel or anti-parallel) and also information about the orientation of elements (any two SSEs can be connected by either left or right chirality). Based on these TOPS diagrams, very fast pattern matching and pattern discovery algorithms for protein topologies were developed by Juris and Gilbert (Viksna and Gilbert, 2001). TOPS Database is accessible from http://www.tops.leeds.ac.uk.

Currently, our project is focused on significant graph-based algorithm development for TOPS Database to enhancing topological protein models with sequence information (from structure based sequence annotation for example by JOY.5, (Mizuguchi et.al., 1998) ) and important biochemical features (such as functional information and lingands and their binding informations) (refer figure:2) that will lead to structure-sequence-function relationships.

Interesting results would be valuable information to predict protein structure and function from sequence, and these problems remain key challenges of direct relevance to project in structural and functional genomics.

(For the figures see web representation of the poster abstracts)
[1] Viksna and Gilbert, (2001) Pattern matching and pattern discovery algorithms for protein topologies, Algorithms in Bioinformatics: First International Workshop, WABI 2001 Proceedings, LNCS 2149 pp 98-111, ISBN 3-540-42516-0.
[2] Gilbert et.al., (1999) Motif-based searching in TOPS protein topology databases. Bioinformatics, 15:317-326. ISSN 1367-4803.
[3] Westhead et.al., (1999) Protein structural topology: automated analysis, diagrammatic representation and database searching. Protein Sci 8, 897-904.
[4] Mizuguchi et.al., (1998) JOY: Protein sequence-structure representation and analysis. Bioinformatics 41:617-623.