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

AUTOR(ES)

Brannetti, Barbara

FONTE

Oxford University Press

RESUMO

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.

Documentos Relacionados

• The Lipase Engineering Database: a navigation and analysis tool for protein families
• A regulator of G protein signaling interaction surface linked to effector specificity
• Functional modules by relating protein interaction networks and gene expression
• How biologically relevant are interaction-based modules in protein networks?
• Using viral species specificity to define a critical protein/RNA interaction surface