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Dihedral-Angle Information Entropy as a Gauge of Secondary Structure Propensity

Center for Computational and Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400

Correspondence: Address reprint requests to Rigoberto Hernandez, Fax: 404-894-0594; E-mail: hernandez{at}chemistry.gatech.edu.

Protein structural information can be uncovered using an information-theory-based entropy and auxiliary functions by taking advantage of high-quality correlation plots between the dihedral angles around a residue and those between sequential residues. A standard information entropy for a primary sequence has been defined using the values of the probabilities of the most likely dihedral angles along the sequence. The distribution of entropy differences relative to the standard for each protein in a reference set—a sublibrary of the Protein Data Bank at the 90% sequence redundancy level—appears to be nearly Gaussian. It gives rise to an auxiliary checking function whose value signals the extent to which the dihedral angle propensities differ from typical structures. Such deviations can arise either because of incorrect dihedral angle assignments or secondary structural propensities that are atypical of the structures in the reference set. This auxiliary checking function can be readily calculated at the public website, http://www.d2check.gatech.edu. Its utility is demonstrated here in an analysis displaying differences between experimentally and theoretically derived structures, and in the analysis of structures derived by homology modeling. A comparison of the new measure, D₂Check, to other checking functions based on backbone conformation—namely, PROCHECK and WHAT_CHECK—is also provided.