ProRule: a new database containing functional and structural information on PROSITE profiles

MOTIVATION Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. SUMMARY We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains. AVAILABILITY ProRule can be accessed through ScanProsite at http://www.expasy.org/tools/scanprosite. A file containing the rules will be made available under the PROSITE copyright conditions on our ftp site (ftp://www.expasy.org/databases/prosite/) by the next PROSITE release.

[1]  T. Stradal,et al.  CH domains revisited , 1998, FEBS letters.

[2]  M. Raida,et al.  The disulfide bond pattern of catrocollastatin C, a disintegrin‐like/cysteine‐rich protein isolated from Crotalus atrox venom , 2000, Protein science : a publication of the Protein Society.

[3]  Philipp Bucher,et al.  Mmsearch: a Motif Arrangement Language and Search Program , 2001, Bioinform..

[4]  Amos Bairoch,et al.  PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors , 2002, Briefings Bioinform..

[5]  J. M. Chong,et al.  Disulfide Bond Assignments of Secreted Frizzled-related Protein-1 Provide Insights about Frizzled Homology and Netrin Modules* , 2002, The Journal of Biological Chemistry.

[6]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[7]  Anne-Lise Veuthey,et al.  Automated annotation of microbial proteomes in SWISS-PROT , 2003, Comput. Biol. Chem..

[8]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[9]  Amos Bairoch,et al.  Recent improvements to the PROSITE database , 2004, Nucleic Acids Res..

[10]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[11]  Amos Bairoch,et al.  Swiss-Prot: Juggling between evolution and stability , 2004, Briefings Bioinform..

[12]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2005, Nucleic Acids Res..

[13]  Zhilei Chen,et al.  A highly sensitive selection method for directed evolution of homing endonucleases , 2005, Nucleic acids research.