A simple method for predicting the secondary structure of globular proteins: implications and accuracy

• Published in: Bioinformatics Vol. 4; no. 3; pp. 357 - 365
• Main Authors: Gascuel, O., Golmard, J. L.
• Format: Journal Article
• Language: English
• Published: Washington, DC Oxford University Press 01.08.1988; Oxford
• Subjects: Algorithms; Amino Acid Sequence; Analytical, structural and metabolic biochemistry; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Mathematical Computing; Protein Conformation; Proteins; Software; PASCAL language; Prediction; Software; Mathematical model; Secondary structure; Algorithm; Aminoacid sequence; Microcomputer; Globular protein
• ISSN: 1367-4803; 0266-7061; 1460-2059
• DOI: 10.1093/bioinformatics/4.3.357

A method is presented for predicting the secondary structure of globular proteins from their amino acid sequence. It is based on a rigorous statistical exploitation of the well-known biological fact that the amino acid compositions of each secondary structure are different. We also propose an evaluation process that allows us to estimate the capacity of a method to predict the secondary structure of a new protein which does not have any homologous proteins whose structure is already known. This evaluation process shows that our method has a prediction accuracy of 58.7% over three states for the 62 proteins of the Kabsch and Sander (1983a) data bank. This result is better than that obtained by the most widely used methods—Lim (1974), Chou and Fasman (1978) and Garnier et al. (1978)—and also than that obtained by a recent method based on local homologies (Levin et al., 1986). Our prediction method is very simple and may be implemented on any microcomputer and even on programmable pocket calculators. A simple Pascal implementation of the method prediction algorithm is given. The interpretation of our results in terms of protein folding and directions for further work are discussed.