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. 2003 Jul 1;31(13):3709-11.
doi: 10.1093/nar/gkg592.

iSPOT: A web tool to infer the interaction specificity of families of protein modules

Barbara Brannetti  1 , Manuela Helmer-Citterich
Affiliations

iSPOT: A web tool to infer the interaction specificity of families of protein modules

Barbara Brannetti et al. Nucleic Acids Res. .

Abstract

iSPOT (http://cbm.bio.uniroma2.it/ispot) is a web tool developed to infer the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from position-specific contacts, derived from the available domain/ligand complexes of known structure, and experimental interaction data to build a database of residue-residue contact frequencies. iSPOT is available to infer the interaction specificity of PDZ, SH3 and WW domains. For each family of protein domains, iSPOT evaluates the probability of interaction between a query domain of the specified families and an input protein/peptide sequence and makes it possible to search for potential binding partners of a given domain within the SWISS-PROT database. The experimentally derived interaction data utilized to build the PDZ, SH3 and WW databases of residue-residue contact frequencies are also accessible. Here we describe the application to the WW family of protein modules.

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Figures

Figure 1
Figure 1
iSPOT home page (http://cbm.bio.uniroma2.it/ispot). iSPOT features are accessible for each family of protein modules by clicking on the name of the family.
Figure 2
Figure 2
WW domains prediction form. The list of all the available WW domains is reported. For each WW domain, the name of the protein and domain range sequence are reported as in the Pfam multiple alignment. Links to the InterPro, Pfam and SMART pages dedicated to the WW domains are available. A further link is provided for submitting lists of SWISS-PROT–TrEMBL accession codes.
Figure 3
Figure 3
Example of an output returned to the user. The WW domains are ranked according to their evaluated propensity to bind any peptides within the input sequence. For each eight-residue long peptide, the peptide sequence and position in the protein are listed. Then the score and the name of the WW domain used for the prediction are reported. The input sequence is reported as well, together with the number of all residues contained and, in case, the number of the non-supported characters (see the on-line documentation). A button is present for immediate submission of the query sequence to the SMART server.
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References

    1. Pawson T. and Nash,P. (2000) Protein–protein interactions define specificity in signal transduction. Genes Dev., 14, 1027–1047. - PubMed
    1. Gribskov M., McLachlan,A.D. and Eisenberg,D. (1987) Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA, 84, 4355–4358. - PMC - PubMed
    1. Gribskov M. and Veretnik,S. (1996) Identification of sequence pattern with profile analysis. Methods Enzymol., 266, 198–212. - PubMed
    1. Weng S., Dong,Q., Balakrishnan,R., Christie,K., Costanzo,M., Dolinski,K., Dwight,S.S., Engel,S., Fisk,D.G., Hong,E. et al. (2003) Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res., 31, 216–218. - PMC - PubMed
    1. Gattiker A., Gasteiger,E. and Bairoch,A. (2002) ScanProsite: a reference implementation of a PROSITE scanning tool. Appl. Bioinf., 1, 107–108. - PubMed

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