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The HSSP database of protein structure-sequence alignments and family profiles
C Dodge1, R Schneider, C Sander
1European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge CB10 1SD, UK.
Nucleic Acids Research
|February 21, 1998
Summary
The HSSP database integrates protein structure and sequence data, offering alignments and profiles for known protein structures. This resource aids in predicting protein structures and understanding protein families.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein science
Background:
- Protein Data Bank (PDB) provides known 3D protein structures.
- SWISS-PROT is a comprehensive protein sequence database.
- Understanding protein structure-sequence relationships is crucial in biology.
Purpose of the Study:
- To create a derived database (HSSP) merging 3D structure and 1D sequence information.
- To provide multiple sequence alignments and sequence profiles for proteins with known 3D structures.
- To facilitate the prediction of secondary and tertiary structures for a large portion of SWISS-PROT sequences.
Main Methods:
- Utilizing data from the Protein Data Bank (PDB) for known 3D protein structures.
- Performing iterative database searches in SWISS-PROT using the MaxHom method.
- Applying position-weighted dynamic programming for sequence profile alignment.
Main Results:
- HSSP database provides aligned sequence families for PDB proteins.
- Sequence profiles characteristic of protein families are generated, centered on known structures.
- The database implies secondary and tertiary structures for 33% of SWISS-PROT sequences.
Conclusions:
- HSSP is a valuable resource for structural bioinformatics, linking known structures to homologous sequences.
- The database enhances the understanding of protein families and aids in structure prediction.
- Frequent updates ensure the HSSP database remains a current and relevant tool for researchers.