The invention provides systems and methods for generating 3D binding consensus pharmacophores. Initially, peptide screening sequence data is aligned. For one or more positions of the alignment: an observed distance matrix describing a distance between the relative binding activity of pairwise comparisons of each amino acid at the selected position is constructed, the observed distance matrix is compared to a plurality of field-based amino acid substitution matrices having the same shape as the observed distance matrix, preferred amino acid substitution matrices are identified from the plurality of amino acid substitution matrices based on the comparison, and a plurality of characteristics for the selected position are identified using the preferred amino acid substitution matrices. Characteristics for a plurality of positions of the alignment are used to generate three-dimensional peptide structures that represent predicted binding conformations. Molecular field information for these structures is clustered to determine a consensus field pharmacophore.

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