BSDD: Biomolecules Segment Display Device--a web-based interactive display tool

Abstract

An interactive web-based display tool, Biomolecules Segment Display Device (BSDD), has been developed to search for and visualize a user-defined motif or fragment among the protein structures available in the Protein Data Bank (PDB). In addition, the tool works for the structures available in a selected sub-set of non-homologous protein structures (25% and 90% sequence identity). The graphics package RASMOL has been incorporated as an interface to visualize the three-dimensional structure of the user-defined motif. In addition, the software can be used to extract the atomic coordinates of the required fragment and save them to the client system. The atomic coordinates are updated every week from the RCSB-PDB server, and hence the results produced by BSDD are up to date at any given time. The software BSDD is available over the World Wide Web at http://iris.physics.iisc.ernet.in/bsdd or http://144.16.71.2/bsdd.

Figure 1

Typical output for pattern matching using ‘Sequences derived using the atomic coordinates’ from the non-homologous (25% identity) sequence database.

Figure 2

A sample output frame for a consensus pattern search. The string CCXXHXXC is used for a pattern matching search. The search string is shown as a ribbon representation, while only the backbone trace is shown for the remaining part of the protein model. To visualize other regions, the user needs to change the residue number in the menu box provided at the bottom of the RASMOL window box.