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Related Experiment Videos

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

P Selvarani1, V Shanthi, C K Rajesh

  • 1Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.

Nucleic Acids Research
|June 25, 2004
PubMed
Summary
This summary is machine-generated.

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A new tool, the Biomolecules Segment Display Device (BSDD), allows users to search and visualize protein motifs within the Protein Data Bank (PDB). This interactive web-based software provides up-to-date structural data and atomic coordinates for protein fragments.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • The Protein Data Bank (PDB) is a crucial repository for protein structure data.
  • Identifying and visualizing specific motifs or fragments within protein structures is essential for understanding protein function and design.
  • Existing tools may lack interactive visualization or comprehensive search capabilities for user-defined fragments.

Purpose of the Study:

  • To develop an interactive web-based tool for searching and visualizing user-defined motifs or fragments in protein structures.
  • To provide access to updated structural data from the Protein Data Bank (PDB).
  • To enable the extraction and saving of atomic coordinates for identified protein fragments.

Main Methods:

  • Development of an interactive web-based display tool named Biomolecules Segment Display Device (BSDD).

Related Experiment Videos

  • Integration of the RASMOL graphics package for three-dimensional visualization of motifs.
  • Implementation of weekly updates of atomic coordinates from the RCSB-PDB server.
  • Inclusion of functionality to search within the full PDB and selected non-homologous subsets (25% and 90% sequence identity).

    • Main Results:

    • The Biomolecules Segment Display Device (BSDD) enables users to search for and visualize specific protein motifs or fragments.
    • The tool provides interactive 3D visualization of user-defined motifs using RASMOL.
    • Atomic coordinates of fragments can be extracted and saved, with data updated weekly for accuracy.

    Conclusions:

    • The Biomolecules Segment Display Device (BSDD) offers a valuable resource for researchers studying protein structures.
    • The tool facilitates the exploration and analysis of protein fragments and motifs.
    • BSDD provides up-to-date and accessible data for structural bioinformatics research.