Abstract
Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool (accessible at http://cbm.bio.uniroma2.it/iSPOT) developed for the prediction of protein-protein interaction mediated by families of peptide recognition modules. iSPOT accesses a database of position specific residue-residue interaction frequencies for members of the SH3 and PDZ protein domain families. The software utilises this database to provide a score for any potential domain peptide interaction. iSPOT: 1. evaluates the likelihood of the interaction between any of the peptides contained in an input protein and a list of domains of the two different families; 2. searches in the SWISS-PROT database for potential partners of a query domain; and 3. has access to a repository of all the domain/target peptide interaction data.
Highlights
The formation of protein complexes is often mediated by families of protein modules that are found repeatedly in the proteome and that have evolved to recognize specific protein surface features
(unlike techniques based on molecular dynamics) SPOT does not require that the domain three-dimensional structure is available and provides a prediction as long as the sequence of the domain member under study can be confidently aligned to a domain of known structure from the same family
The reliability of the prediction depends on the level of sequence identity, in the region involved in target recognition, between the query domain and the domains whose experimentally determined binding data have been used to train the software
Summary
The formation of protein complexes is often mediated by families of protein modules that are found repeatedly in the proteome and that have evolved to recognize specific protein surface features. The SPOT procedure [1] was developed to provide a software tool that would elaborate on the experimental data obtained by screening peptide repertoires in order to infer the recognition specificity of any element of a protein module family. The application of SPOT, in contrast to profile and pattern matching methods, is not restricted to domains for which experimental binding data is available.
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