2 ArticleAnalysis of the Accuracy and Implications of Simple Methods for Predicting the Secondary Structure of Globular ProteinsJ. Garnier, D.J. Osguthorpe and B RobsonJournal of Molecular Biology (1978); 120,
3 Introduction Predict secondary structure from aa-sequence alone Simple predictive algorithmFour-state predictionsMore additional information enhances prediction
4 Theory Predict conformational state of each residue in a sequence I(Sj; R1, R2, … Rlast)Effect of one residue affects conformation up to eight residues distant20 X 4 X 17 parameters
5 Method Each amino acid is predicted to exist in one of four states: 1) H = helix2) C = coil3) T = turn4) E = extended chain (beta-strand)Each residue is given a score based upon the nature and positions of the ± 8th residues according to previously calculated tables.The residue receives a score for each of the conformational possibilities and the highest one gives the prediction.
6 ExampleArg-Gly-Ser-Ala-Lys-Cys-Trp-Tyr-Pro-Ala-Val-Gly-Glu-Lys-Asp-Met-IleThe Pro residue would receive the following scores based on the previously calculated tables:
7 Advantages/Disadvantages Better predictionsLong-range interactions5 to 10% improvement with homology studiesOnly 63% correctDepends on databasethe GOR method is an approximation