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Nature Biotechnology 26, 1041–1045 (1 September 2008) | doi:10.1038/nbt.1489

Predicting PDZ domain|[ndash]|peptide interactions from primary sequences

Jiunn R Chen , Bryan H Chang , John E Allen , Michael A Stiffler & Gavin MacBeath

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.