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Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL.

S A Teichmann1, C Chothia, G M Church

  • 1MRC Laboratory of Molecular Biology, Cambridge, UK. sat@mrc-lmb.cam.ac.uk

Bioinformatics (Oxford, England)
|June 8, 2000
PubMed
Summary

A new protein sequence search method using an intermediate sequence library (PDB-ISL) offers a faster alternative to iterative methods like PSI-BLAST for structural genomics. This approach significantly speeds up sequence assignment for proteins of known and unknown structures.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Genomics

Background:

  • Large-scale structural assignment to protein sequences is crucial for computational structural genomics.
  • Existing iterative multiple sequence search methods, like PSI-BLAST, can be computationally intensive.
  • A faster, sensitive sequence search procedure is essential for efficient structural genomics.

Purpose of the Study:

  • To develop and evaluate a novel approach using intermediate sequences as a shortcut for iterative multiple sequence search methods.
  • To create a searchable library of intermediate sequences for proteins of known structure (PDB-ISL).
  • To enable rapid sequence similarity searches for proteins of unknown structure.

Main Methods:

  • Construction of the Protein Data Bank Intermediate Sequence Library (PDB-ISL) using sequences of known protein structures as queries against a large sequence database with PSI-BLAST.

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  • Utilizing pairwise sequence comparison methods (e.g., FASTA, BLAST2) to search the PDB-ISL for homologous sequences.
  • Calibrating PDB-ISL searches to ensure comparable accuracy to PSI-BLAST at a given error rate.

    • Main Results:

    • The PDB-ISL enables matching sequences of proteins with unknown structures to distantly related proteins with known structures.
    • Searches using PDB-ISL demonstrate comparable accuracy to PSI-BLAST at similar error rates.
    • The PDB-ISL approach offers significant speed advantages, being approximately 20 times faster for small genomes and several hundred times faster for large genomes compared to PSI-BLAST.

    Conclusions:

    • The PDB-ISL provides a computationally efficient and sensitive method for large-scale protein sequence assignment.
    • This intermediate sequence library approach serves as a viable and faster alternative to iterative search methods for structural genomics.
    • The PDB-ISL accelerates the process of identifying homologous proteins, facilitating structural and functional annotation.