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A new structure-based approach was proposed to quantitatively characterize the binding profile of human amphiphysin-1 (hAmph1) SH3 domain–peptide complexes. In this protocol, the protein/peptide atoms were classified into 16 types in terms of their physicochemical meaning and biological function, and then a 16 × 16 atom-pair interaction matrix was constructed to describe 256 atom-pair types between...
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