Garnier-Osguthorpe-Robson

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Garnier-Osguthorpe-Robson GOR Method

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, 97-120

Introduction Predict secondary structure from aa-sequence alone Simple predictive algorithm Four-state predictions More additional information enhances prediction

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

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.

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:

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