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

• Published in: Biochemistry (Easton) Vol. 22; no. 21; pp. 4894 - 4904
• Main Authors: Cohen, Fred E, Abarbanel, Robert M, Kuntz, I. D, Fletterick, Robert J
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 01.01.1983
• Subjects: algorithms; alpha-helix; amino acid sequences; amino acids; beta-strand; Biological and medical sciences; computer analysis; computer techniques; Fundamental and applied biological sciences. Psychology; hydrophilicity; Isomerism; Macromolecular Substances; Mathematics; Models, Molecular; Molecular biophysics; molecular conformation; physicochemical properties; Protein Conformation; protein structure; Proteins; secondary structure; Structure in molecular biology; Structure-Activity Relationship; Tridimensional structure; turngen; Proteins; Computer program; Tertiary structure; Β-Structure; Helical structure; Secondary structure; Algorithm; Globular protein
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00290a005

We describe an algorithm for assigning the secondary structure of alpha/beta proteins. 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 two 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.