An algorithm for secondary structure determination in proteins based on sequence similarity

FEBS Letters

Levin, Jonathan M.¹  Garnier, Jean¹  Robson, Barry¹ 

[1] Laboratoire de Biochimie physique, INRA, Université de Paris Sud, 91405 Orsay Cédex, France

关键词: Protein structure Secondary structure prediction Amino acid sequence homology;   

DOI  :  10.1016/0014-5793(86)80917-6

学科分类：生物化学/生物物理

来源: John Wiley & Sons Ltd.

【 摘 要 】

A secondary structure prediction algorithm is proposed on the hypothesis that short homologous sequences of amino acids have the same secondary structure tendencies. Comparisons are made with the secondary structure assignments of Kabsch and Sander from X-ray data [(1983) Biopolymers 22, 2577-2637] and an empirically determined similarity matrix which assigns a sequence similarity score between any two sequences of 7 residues in length. This similarity matrix differs in many respects from that of the Dayhoff substitution matrix [(1978) in: Atlas of Protein Sequence and Structure, (Dayhoff M.O. ed). vol. 5. suppl. 3, pp. 353-358, National Biochemical Research Foundation, Washington, DC]. This homologue method had a prediction accuracy of 62.2% over 3 states for 61 proteins and 63.6% for a new set of 7 proteins not in the original data base.

【 授权许可】

Unknown