Pfam, protein database

Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2000 28[l] 263-266. 

The specific format for cross references to the PROSITE and Pfam protein domain and family databases is ... 

Guide Bioinformatics, 1998, 18. Attwood, T. K., The quest to deduce protein function from sequence the role of pattern databases, Int. ]. Biochem. Cell Biol., 2000, 32, 139. Bateman, A., Bieney, E., Durbin, R., Eddy, S. R., Howe, K. L., and Sonnhammbe, E. L., The Pfam Protein Families Database, Nucleic Acids Res., 2000, 28, 263. 

Pfam Protein family database protein families database of aligmnents... 

Protein family used to describe a protein family database. See Persson, B., Bioinformatics in protein analysis, EXS 88, 215-231, 2000 Bateman, A., Bimey, E., Cerruti, L. et al., The Pfam protein families database, Nucl. Acids Res. 30, 276-280, 2002 Lubec, G., Afjehi-Sadat, L., Yang, J.W., and John, J.P, Searching for hypothetical proteins theory and practice based upon original data and literature, Prog. Neurobiol. 77,90-127,2005 Anderston, J.N., Del Vecchio, R.L., Kannan, N. et al., Computational analysis of protein tyrosine phosphatases practical guide to bioinformatics and data resources, Methods 35, 90-114, 2005. 

Bateman, A., Coin, L., Durbin, R., et al. (2004) The Pfam Protein Families Database. Nucleic Acids Res. 32, D138-D141. 

Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD. The Pfam protein families database. Nucl Acids Res. 2012 50 D290-301. 

Sonnhammer, E.L., Eddy, S.R., Durbin, R. Pfam a comprehensive database of protein domain families based on seed alignments. Proteins 28 405-420, 1997. 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

Using the domain databases should be considered an important early step in the analysis of any protein. Several of the domain databases are reviewed next. The reader should be aware that the authors are a part of the Pfam consortium and although we have tried to be impartial, the following will almost certainly be a biased view. 

Pattern and motif analysis Motif Scan PROSITE Pfam http //myhits.isb-sib.ch/cgi-bin/motif scan http //us.expasy.org/prosite/ http //www.sanger.ac.uk/Software/Pfam/ Einding motifs in a sequence. Protein fanulies and domains. Protein fanulies database of hidden Markov models (HMMs). 

A variety of databases and online tools exist to facilitate searches for protein motifs (Table 6). The most comprehensive resource for the detection of large protein motifs is the Conserved Domain Database (CDD) provided by NCBI. The CDD includes all data present in the SMART and PFAM databases, along with some manually curated entries. All protein-protein BLAST... 

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