Conserved Regions can Predict Protein Binding Regions
Raphael Finkel and Heinz Kohler
Affiliation: Dept. of Computer Science and Dept. of Microbiology and Immunology, University of Kentucky, USA.
Keywords: Amino acids, binary code, binding sites, codons, conservation, evolution, genetic code, triplet.
We demonstrate the Binary Identified Contact Domain (BICD) method for predicting binding sites for proteins
that starts with amino-acid sequences of several species, finds regions that are evolutionarily conserved, and weights
regions by their local hydrophilicity. The measure of conservation takes transversions as significant but transitions as
insignificant, in keeping with a theory of original singlet codes. The BICD method correctly predicts several known
binding sites for the BRCA2 protein with PABL2 and RAD51 as well as the binding sites of the MDM2-P53 complex.
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