A simple method for predicting the secondary structure of globular proteins: implications and accuracy
Authors:
- J. L. GolmardJGJ. L. Golmard
- 1 January 1988
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 4 (3) , 357-365
Abstract
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 homolgous 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.sbd.Lim (1974), Chou and Fasman (1978) and Garnier et al. (1978).sbd. 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.Keywords
This publication has 10 references indexed in Scilit:
- Prediction of protein structural class from the amino acid sequenceBiopolymers, 1986
- Evolutionary similarity among peptide segments is a basis for prediction of protein foldingBiopolymers, 1986
- Amino acid sequence homology applied to the prediction of protein secondary structures, and joint prediction with existing methodsBiochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1986
- The Folding Type of a Protein Is Relevant to the Amino Acid CompositionThe Journal of Biochemistry, 1986
- The hydrophobic moment detects periodicity in protein hydrophobicity.Proceedings of the National Academy of Sciences, 1984
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 1983
- Secondary structure assignment for .alpha./.beta. proteins by a combinatorial approachBiochemistry, 1983
- Prediction of protein antigenic determinants from amino acid sequences.Proceedings of the National Academy of Sciences, 1981
- PREDICTION OF THE SURFACE‐INTERIOR DIAGRAM OF GLOBULAR PROTEINS BY AN EMPIRICAL METHODInternational Journal of Peptide and Protein Research, 1980
- Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteinsJournal of Molecular Biology, 1978