This article presents a mathematical model on the design of peptide inhibitors for proteins. This model is a combination of the two rules on protein-ligand interaction, Miyazawa-Jernigan (M-J) matrix and hidden Markov model (HMM). The model is applied to predict peptide inhibitors for the protein cyclophilin A (CypA) and FKBP12, and then validated by the highest occupied molecular orbital calculation, dock process between protein and inhibitor, and biological experiments. The results are encouraging and suggest that we have taken a step forward towards building a mathematical theory on the design of peptide inhibitors for proteins. The mathematical model is rough at present, but if it represents a correct direction of the theoretical trends of biology as we believe, then this theory can be further developed and become more and more precise.
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