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An all‐atom, distance‐dependent scoring function for the prediction of protein–DNA interactions from structure

We have developed an all‐atom statistical potential function for the prediction of protein–DNA interactions from their structures, and show that this method outperforms similar, lower‐resolution statistical potentials in a series of decoy discrimination experiments. The all‐atom formalism appears to capture details of atomic interactions that are missed by the lower‐resolution methods, with the majority of the discriminatory power arising from its description of short‐range atomic contacts. We show that, on average, the method is able to identify 90% of near‐native docking decoys within the best‐scoring 10% of structures in a given decoy set, and it compares favorably with an optimized physical potential function in a test of structure‐based identification of DNA binding‐sequences. These results demonstrate that all‐atom statistical functions specific to protein–DNA interactions can achieve great discriminatory power despite the limited size of the structural database. They also suggest that the statistical scores may soon be able to achieve accuracy on par with more complex, physical potential functions. Proteins 2007. © 2006 Wiley‐Liss, Inc.