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Related Experiment Videos

The HSSP database of protein structure-sequence alignments

R Schneider1, C Sander

  • 1Protein Design Group, European Molecular Biology Laboratory, Heidelberg, Germany.

Nucleic Acids Research
|January 1, 1996
PubMed
Summary

The HSSP database integrates protein 3-D structures with sequence alignments of homologous proteins. This resource provides insights into protein families and their implied structures, covering a significant portion of known protein sequences.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein sequence analysis

Background:

  • The Protein Data Bank (PDB) provides crucial 3-D structural data for proteins.
  • Sequence databases like SwissProt store vast amounts of protein sequence information.
  • Integrating structural and sequence data is vital for understanding protein function and evolution.

Purpose of the Study:

  • To create a comprehensive database (HSSP) merging protein 3-D structural information with sequence data.
  • To provide multiple sequence alignments and characteristic sequence profiles for protein families.
  • To enable the prediction of secondary and tertiary structures for homologous proteins.

Main Methods:

  • Utilizing protein structures from the Protein Data Bank (PDB).

Related Experiment Videos

  • Performing database searches in SwissProt using homologous sequences.
  • Employing a position-weighted dynamic programming method (MaxHom) for sequence profile alignment.

    • Main Results:

    • The HSSP database successfully merges 3-D structural data with 1-D sequence information.
    • It provides multiple sequence alignments and sequence profiles for protein families.
    • The database implies secondary and tertiary structures for homologous proteins, covering 27% of SwissProt sequences.

    Conclusions:

    • HSSP serves as a valuable resource for studying protein structure-function relationships.
    • The database facilitates the exploration of protein families and their evolutionary relationships.
    • It offers a powerful tool for predicting protein structures based on sequence homology.