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Related Experiment Videos

The HSSP database of protein structure-sequence alignments

R Schneider1, A de Daruvar, C Sander

  • 1Protein Design Group, European Molecular Biology Labratory, D-69012 Heidelberg, Germany. schneider@embl-heidelberg.de

Nucleic Acids Research
|January 1, 1997
PubMed
Summary
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The HSSP database integrates protein structural and sequence data, providing alignments of homologous sequences and their implied structures. This resource aids in understanding protein families and their three-dimensional conformations.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • The Protein Data Bank (PDB) contains experimentally determined protein structures.
  • SwissProt is a curated protein sequence database.
  • Understanding protein structure-sequence relationships is crucial in molecular biology.

Purpose of the Study:

  • To create a comprehensive database merging protein structural and sequence information.
  • To provide aligned sequence families with implied secondary and tertiary structures.
  • To enhance the utility of protein structural data by linking it to sequence homology.

Main Methods:

  • Developed HSSP (Homology-derived Secondary Structure of Proteins) database.
  • Integrated 3-D structural data from PDB with 1-D sequence data from SwissProt.

Related Experiment Videos

  • Utilized position-weighted dynamic programming (MaxHom) for sequence profile alignment to identify homologous sequences.
  • Frequently updated database content.

    • Main Results:

    • HSSP database merges structural (3-D) and sequence (1-D) information for proteins.
    • For each PDB protein, it provides multiple sequence alignments of homologues and characteristic sequence profiles.
    • Identified homologous sequences are likely to share the same 3-D structure as the PDB entry.
    • Implied secondary and tertiary structures are provided for 29% of SwissProt sequences.

    Conclusions:

    • HSSP serves as a valuable resource for studying protein families and their structures.
    • The database facilitates the prediction of protein structures based on sequence homology.
    • It bridges the gap between sequence databases and structural information, expanding structural insights to a larger protein set.