Protein domain, family and function databases
Protein molecules play functions in living organisms. They are usually
classified into families based on the different functions they play. Proteins
in the same family or subfamily often have conserved sequence motifs or
finger prints, as well as ungapped blocks or functional domains. With the
great amount of available sequence data, secondary databases of protein
molecules have been constructed. We select some of them for this course.
Protein domain databases
- Prosite - A database of
protein domains, families and functional sites, created and maintained
by the Swiss Institute of Bioinformatics.
- PRINTS
- A database of protein fingerprints consisting of conserved motifs within
a protein family, created and maintained by Manchester University, UK.
- BLOCKS - A database of multiply
aligned ungapped segments corresponding to the most highly conserved regions
of proteins, created and maintained by the Fred Hutchinson Cancer Research
Center, US.
- CDD
- A database of conserved protein domains created and maintained by the
NCBI structure group.
- ProDom
- A database of comprehensive set of protein domain families automatically
generated from the SWISS-PROT and TrEMBL sequence databases, developed
and maintained by the University Claude Bernard, France.
Protein family databases
- PFam - A database of protein
families represented by multiple sequence alignments and hidden Markov
models, constructed and maintained by the Sanger Institute, UK.
Protein function databases
- IMGT - The international immunogenetics
information system a high-quality integrated knowledge resource of the
immune system of human and other vertebrate species, created and maintained
by University of Montpellier, France.
- HPA - A web site for the
the human protein atlas which shows expression and localization of proteins
in a large variety of normal human tissues, cancer cells and cell lines
with the aid of immunohistochemistry images, developed and maintained
by Proteome Resource Center, Sweden.
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| 16 July 2008, J Luo, CBI, PKU, Beijing, China