AI Article Synopsis
- iSPOT is a web tool designed to predict how specific protein module families, like PDZ, SH3, and WW domains, recognize and interact with other proteins and peptides.
- It uses a method called the SPOT procedure, which analyzes structural data from known domain/ligand complexes alongside experimental data to create a database of residue contact frequencies.
- Users can input a domain and a protein/peptide sequence to evaluate interaction probabilities, as well as search for potential binding partners within the SWISS-PROT database.
Article 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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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168998 | PMC |
| http://dx.doi.org/10.1093/nar/gkg592 | DOI Listing |
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