BSDD: Biomolecules Segment Display Device—a web-based interactive display tool
1 Bioinformatics Centre and 2 Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
* To whom correspondence should be addressed. Tel: +91 080 22933059; Fax: +91 080 23600551; Email: sekar{at}physics.iisc.ernet.in
This work is dedicated to Professor M. Vijayan, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
Received February 10, 2004; Revised and Accepted April 5, 2004
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.
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