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Short Commentary on: On the Prediction of DNA-binding Preferences of C2H2-ZF Domains Using Structural Models: Application on Human CTCF

Alberto Meseguer, Ruben Molina-Fernández, Narcis Fernandez-Fuentes, Oriol Fornes*, Baldo Oliva*

In the work entitled “On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF” we present a new computational method to predict the DNA-binding preferences for Cis2-His2 zinc finger (C2H2-ZF) protein-domains from their amino acid sequence or structure. The method uses the structures of protein-DNA complexes to calculate a set of knowledge-based statistical potentials. Given the low numbers of protein-DNA complexes with known structure, we supplement the set of structures with experimental yeast-one-hybrid interactions of more than 170000 sequence-designed C2H2-ZF domains. We have implemented a server to model the structure of any protein-DNA complex of this family and derive its theoretical Position Weight Matrix based on the best scores of interactions calculated with the statistical potentials. The approach is validated and applied to the human sequence of CTCF.