Secondary structure assignment for .alpha./.beta. proteins by a combinatorial approach

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Abstract
An algorithm for assigning the secondary structure of .alpha./.beta. proteins is described. Turns are identified very accurately (98%) by simultaneously considering hydrophilicity and the ideal spacing of turns throughout the sequence. The segments bounded by these turns are labeled by a pattern-recognition scheme based on the physical properties of .alpha.-helices and .beta.-strands, in this class of proteins. Long-range, as well as local, information is incorporated to enhance the quality of the assignments. Although the assignment for any one sequence is not unique, at least one of the assignments bears a close resemblance to the native structure. The algorithm successfully divides protein sequences into 2 classes: .alpha./.beta. and non-.alpha./.beta.. The accuracy of the secondary-structure assignments in the .alpha./.beta. class is sufficient to provide useful input for tertiary-structure assignments.