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CKAAPs DB: a Conserved Key Amino Acid Positions DataBase.

Wilfred W Li1, Boojala V B Reddy, John G Tate

  • 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
|December 26, 2001
PubMed
Summary

The updated 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 by highlighting residues vital for folding, stability, and function.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Proteins with similar structures can have divergent sequences.
  • Identifying conserved key amino acid positions (CKAAPs) is crucial for understanding protein folding, stability, and function.
  • CKAAPs are valuable for protein engineering applications.

Purpose of the Study:

  • To provide an updated version of the Conserved Key Amino Acid Positions DataBase (CKAAPs DB).
  • To enhance the analysis and visualization of CKAAPs.
  • To improve search functionalities and user interaction for CKAAPs analysis.

Main Methods:

  • Analysis of structurally similar proteins with dissimilar sequences using CE and FSSP databases.
  • Mapping CKAAPs onto Protein Data Bank (PDB) structures visualized with Molscript.

Related Experiment Videos

  • Structure-based and secondary structure alignments highlighting CKAAPs.
  • Sequence homolog visualization using Mview with color-coded identities and property groups.
  • Implementation of new search options and a custom CKAAPs analysis interface.

    • Main Results:

    • CKAAPs DB now includes spatial context by mapping CKAAPs onto PDB structures.
    • Enhanced visualization options for CKAAPs within various alignment types.
    • Expanded search capabilities including keywords, PDB IDs, EC numbers, and Gene Ontology.
    • A new user interface for custom CKAAPs analysis and retrieval.

    Conclusions:

    • The updated CKAAPs DB offers improved tools for exploring conserved residues in proteins.
    • Enhanced visualization and search functionalities facilitate deeper insights into protein structure-function relationships.
    • The database serves as a valuable resource for protein engineering and structural biology research.