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Presentation on theme: "Garnier-Osguthorpe-Robson"— Presentation transcript:

1 Garnier-Osguthorpe-Robson
GOR Method

2 Article Analysis of the Accuracy and Implications of Simple Methods for Predicting the Secondary Structure of Globular Proteins J. Garnier, D.J. Osguthorpe and B Robson Journal of Molecular Biology (1978); 120,

3 Introduction Predict secondary structure from aa-sequence alone
Simple predictive algorithm Four-state predictions More 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 distant 20 X 4 X 17 parameters

5 Method Each amino acid is predicted to exist in one of four states:
1) H = helix 2) C = coil 3) T = turn 4) 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 Example Arg-Gly-Ser-Ala-Lys-Cys-Trp-Tyr-Pro-Ala-Val-Gly-Glu-Lys-Asp-Met-Ile The Pro residue would receive the following scores based on the previously calculated tables:

7 Advantages/Disadvantages
Better predictions Long-range interactions 5 to 10% improvement with homology studies Only 63% correct Depends on database the GOR method is an approximation

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