Transcript G Protein Coupled Receptors

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-GluLys-Asp-Met-Ile
The Pro residue would receive the following scores based on
the previously calculated tables:
Advantages/Disadvantages
• Better predictions
• Only 63% correct
• Long-range
interactions
• Depends on database
• 5 to 10% improvement
with homology studies
• the GOR method is an
approximation