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Related Experiment Videos

PSSARD: protein sequence-structure analysis relational database.

Kunchur Guruprasad1, K Srikanth, A V N Babu

  • 1Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad 500007, Andhra Pradesh, India. guru@ccmb.res.in

International Journal of Biological Macromolecules
|August 2, 2005
PubMed
Summary
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A new relational database provides amino acid sequences and secondary structures for proteins with less than 25% sequence identity. This resource aids in retrieving sequences compatible with super-secondary structure conformations.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Understanding protein structure-function relationships is crucial in molecular biology.
  • Databases of protein sequences and structures are essential tools for researchers.
  • Identifying homologous proteins with diverse sequences but similar structures is challenging.

Purpose of the Study:

  • To create a curated relational database of amino acid sequences and their corresponding secondary structures.
  • To facilitate the retrieval of protein sequences based on structural similarity, irrespective of sequence identity.
  • To provide a valuable resource for studying protein architecture and super-secondary structures.

Main Methods:

  • Implemented a relational database using protein crystal structure data from the Protein Data Bank (PDB).

Related Experiment Videos

  • Selected representative amino acid sequences using the PDB_SELECT program, ensuring <25% pairwise sequence identity.
  • Extracted secondary structure information directly from the PDB website.

    • Main Results:

    • The database contains protein descriptions, PDB codes, crystal structure resolution, residue counts, amino acid sequences, and secondary structure details.
    • The dataset is freely accessible and searchable across multiple fields.
    • The database effectively allows retrieval of amino acid sequences compatible with specific super-secondary structure conformations.

    Conclusions:

    • The developed database serves as a unique resource for structural bioinformatics research.
    • It enables efficient exploration of sequence-structure relationships, particularly for super-secondary structures.
    • The accessibility and query capabilities of the database enhance its utility for the scientific community.