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CKAAPs DB: a conserved key amino acid positions database.

W W Li1, B V Reddy, I N Shindyalov

  • 1San Diego Supercomputer Center and Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA.

Nucleic Acids Research
|January 11, 2000
PubMed
Summary

The Conserved Key Amino Acid Positions DataBase (CKAAPs DB) identifies crucial amino acid residues in proteins with similar structures but different sequences. This resource aids protein engineering and modeling by highlighting residues potentially vital for protein folding, stability, and function.

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Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Science

Background:

  • Proteins with similar structures can exhibit significant sequence divergence.
  • Identifying conserved residues across these dissimilar sequences is challenging but important.
  • Key residues are hypothesized to be critical for protein folding, stability, and function.

Purpose of the Study:

  • To introduce the Conserved Key Amino Acid Positions DataBase (CKAAPs DB).
  • To provide a resource for identifying key residues in structurally similar proteins with varying sequences.
  • To support protein engineering and modeling efforts.

Main Methods:

  • Analysis of pairwise structure alignments to identify conserved key amino acid positions (CKAAPs).
  • Integration of data from Combinatorial Extension (CE) and FSSP databases.

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  • Development of a web-accessible relational database for querying and retrieval.

    • Main Results:

    • The CKAAPs DB contains analyses for over 170 substructures across approximately 3000 representative polypeptide chains.
    • The database includes CKAAPs for over 5000 representative polypeptide chains, covering all known Protein Data Bank (PDB) structures.
    • A web interface allows querying by PDB ID, protein name, function, and Enzyme Classification number.

    Conclusions:

    • CKAAPs DB offers a valuable resource for researchers studying protein structure-function relationships.
    • The identified CKAAPs can guide experimentalists and theoreticians in protein engineering and modeling.
    • The database facilitates the exploration of conserved residues critical for protein properties.