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The Pfam protein families database
Alex Bateman1, Ewan Birney, Lorenzo Cerruti
1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. agb@sanger.ac.uk
Nucleic Acids Research
|December 26, 2001
Summary
Pfam, a protein family database, now includes structural domain data and active site information. This protein sequence alignment resource enhances protein annotation and offers new search functionalities.
Area of Science:
- Bioinformatics
- Structural Biology
- Computational Biology
Background:
- Pfam is a comprehensive database of protein families.
- It contains multiple sequence alignments and profile hidden Markov models.
- The database is accessible globally via the World Wide Web.
Purpose of the Study:
- To enhance the Pfam database with structural domain information.
- To improve domain-based annotation of proteins.
- To expand the functionality and usability of the Pfam resource.
Main Methods:
- Utilized available structural data to align Pfam families with structural domains.
- Incorporated predictions of non-domain regions.
- Augmented multiple sequence alignments with secondary structure and active site residue markup.
Main Results:
- The latest version (6.6) contains 3071 protein families.
- Pfam families now correspond with structural domains, improving annotation.
- New search tools, including taxonomy search and domain query, have been added.
Conclusions:
- Pfam provides an enhanced resource for protein family analysis.
- The integration of structural data and new search tools increases its utility.
- Pfam facilitates deeper understanding of protein structure and function.