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Related Experiment Videos

The PSSH database of alignments between protein sequences and tertiary structures.

Andrea Schafferhans1, Joachim E W Meyer, Seán I O'Donoghue

  • 1Lion Bioscience AG, Waldhoferstrasse 98, 69123 Heidelberg, Germany.

Nucleic Acids Research
|January 10, 2003
PubMed
Summary

We introduce the Protein Sequence-to-Structure Homologies (PSSH) database, an inverse of the HSSP database. PSSH links protein sequences to their related 3D structures, improving navigation and feature mapping.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The Homology-derived Secondary Structure of Proteins (HSSP) database links 3D structures to related protein sequences.
  • Accessing structural information from a sequence perspective requires an inverse approach.

Purpose of the Study:

  • To introduce the Protein Sequence-to-Structure Homologies (PSSH) database, an inverse of the HSSP database.
  • To present derived databases HSSPchain and HSSPalign for enhanced sequence-structure relationship exploration.
  • To facilitate easier navigation from protein sequences to their corresponding 3D structures and mapping of sequence features onto structures.

Main Methods:

  • Derivation of the PSSH database from the improved HSSP2 database.
  • Development of HSSPchain to list sequences related to a specific PDB chain.

Related Experiment Videos

  • Creation of HSSPalign for detailed sequence-to-structure alignments.

    • Main Results:

    • PSSH provides structural information for over 400,000 protein sequences (48% SWALL, 61% SWISS-PROT) as of September 2002.
    • HSSPchain contains sequence information for over 25,000 PDB chains.
    • HSSPalign offers over 14 million sequence-to-structure alignments.

    Conclusions:

    • The PSSH database and its derivatives offer a novel, sequence-centric view of protein structure relationships.
    • These databases significantly enhance the ability to navigate and analyze sequence-structure connections.
    • The new resources are accessible via SRS 3D, improving data discoverability for researchers.