Quantitative Structure–Activity Relationship Model for Prediction of Protein–Peptide Interaction Binding Affinities between Human Amphiphysin-1 SH3 Domains and Their Peptide Ligands

Protein–protein interaction plays a critical role in signal transduction and many other key biological processes. The present study evaluated four parameters selected from among 554 physiochemical variables of 20 natural amino acids listed in AAindex, namely, hydrophobicity, electronic properties, steric properties, and hydrogen-bond properties. Human amphiphysin-1 Src homology 3 (SH3) domain-binding decapeptides were the object of analysis. A quantitative structure–activity relationship model of the SH3 domain-binding peptides was constructed using multivariate linear regression. The results showed that the four parameters ably characterize the structure of SH3 domain-binding decapeptides, have definitive physicochemical properties and a low level of computational complexity, are accessible, and may be used in integrated prediction models for other protein–peptide interactions.