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

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.

SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules.

SEM, Symmetry Equivalent Molecules, is a web-based graphical user interface to generate and visualize the symmetry equivalent molecules (proteins and nucleic acids). In addition, the program allows the users to save the three-dimensional atomic coordinates of the symmetry equivalent molecules in the local machine. The widely recognized graphics program RasMol has been deployed to visualize the reference (input atomic coordinates) and the symmetry equivalent molecules. This program is written using CGI/Perl scripts and has been interfaced with all the three-dimensional structures (solved using X-ray crystallography) available in the Protein Data Bank. The program, SEM, can be accessed over the World Wide Web interface at http://dicsoft2.physics.iisc.ernet.in/sem/ or http://144.16.71.11/sem/.