PRINTS and its automatic supplement, prePRINTS

Abstract

The PRINTS database houses a collection of protein fingerprints. These may be used to assign uncharacterised sequences to known families and hence to infer tentative functions. The September 2002 release (version 36.0) includes 1800 fingerprints, encoding approximately 11 000 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growth, we report here the development of an automatic supplement, prePRINTS, designed to increase the coverage of the resource and reduce some of the manual burdens inherent in its maintenance. The databases are accessible for interrogation and searching at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.

Figure 1

Illustration of the automated prePRINTS pipeline.

Figure 2

Exerpt from a typical prePRINTS entry (for convenience, the initial and final motifs, and the matched sequence identifiers and accession numbers have been omitted). The example illustrates the fingerprint for apolipoprotein A-I, for which 4 motifs were generated by the prePRINTS pipeline. The fingerprint is ‘clean’, matching 18 sequences completely, with no partial matches, as indicated by the Summary Information. Cross-references have been generated to 6 databases, and 6 literature references have been included, the last two of which relate to crystallographic and NMR structure determinations respectively. The documentation field reports on the function of the protein and its disease associations, together with its structural and familial relationships. Keywords are also provided. In addition, a brief technical description indicates some of the parameters used to create the fingerprint. Except for the Summary Information, which was generated by the fingerprinting process, the rest of the information shown here was created fully automatically by PRECIS.