Fig. 2

Generation of template library containing peptide bound PDZ domains. The set of 267 human PDZ domains identified by te Velthius et al. [24] were mapped onto proteins in UniProt. UniProt ACs could be obtained for 264 PDZ domain containing proteins. For each of these 264 PDZ domains a stretch of residues N-terminus to the domain sequences identified by te Velthius et al. [24] were also included as that region harbored a structurally conserved β sheet. The structural models for each of these 264 PDZ domains in absence of the bound peptide were obtained from SWISS-MODEL. Each of these 264 ligand free PDZ structural models were aligned with the available 38 peptide bound crystal structures of PDZ domains and from nearest peptide bound PDZ domain, the peptide coordinates were transformed after optimal superposition of apo and holo PDZ domain structures. Using this protocol peptide-bound structural model could be obtained for 260 human PDZ domains and remaining four were excluded as they lacked complete 3D structure of the PDZ domain