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Abstract

Provided are systems and methods for generating context-specific, field based amino acid substitution matrices. In some implementations, the systems and methods utilize a set of characteristics including sequence length, sequence, variable position, backbone conformation, sidechain conformation, and charge and/or ionization state to construct a number of instantiated virtual peptide variants that vary an amino acid at the variable position. Molecular fields are then calculated for each instantiated variant. The fields for each variant are then compared to one another in a pairwise fashion. Values representing the similarity of the fields resulting from the comparison are then assembled into an amino acid substitution matrix.

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First Claim