FB2025_01 , released February 20, 2025
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Citation
Chen, J.R., Chang, B.H., Allen, J.E., Stiffler, M.A., MacBeath, G. (2008). Predicting PDZ domain-peptide interactions from primary sequences.  Nat. Biotechnol. 26(9): 1041--1045.
FlyBase ID
FBrf0206812
Publication Type
Research paper
Abstract
PDZ domains constitute one of the largest families of interaction domains and function by binding the C termini of their target proteins. Using Bayesian estimation, we constructed a three-dimensional extension of a position-specific scoring matrix that predicts to which peptides a PDZ domain will bind, given the primary sequences of the PDZ domain and the peptides. The model, which was trained using interaction data from 82 PDZ domains and 93 peptides encoded in the mouse genome, successfully predicts interactions involving other mouse PDZ domains, as well as PDZ domains from Drosophila melanogaster and, to a lesser extent, PDZ domains from Caenorhabditis elegans. The model also predicts the differential effects of point mutations in peptide ligands on their PDZ domain-binding affinities. Overall, we show that our approach captures, in a single model, the binding selectivity of the PDZ domain family.
PubMed ID
PubMed Central ID
PMC2655215 (PMC) (EuropePMC)
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Nat. Biotechnol.
    Title
    Nature biotechnology
    Publication Year
    1996-
    ISBN/ISSN
    1087-0156
    Data From Reference
    Genes (6)