Experiment 6

Aim: Write a program to implement GOR algorithm

Equipment Required: Computer with internet connection and Matlab installed
Learning Objectives: To acquaint students with the Programming skills, to write program
Theory:

The GOR method (Garnier-Osguthorpe-Robson) is an information

theory-based method for the prediction of secondary
structures in proteins.[1] It was developed in the late 1970s shortly
after the simpler Chou-Fasman method. Like Chou-Fasman, the GOR
method is based on probability parameters derived from empirical
studies of known protein tertiary structures solved by X-ray
crystallography. However, unlike Chou-Fasman, the GOR method
takes into account not only the propensities of individual amino
acids to form particular secondary structures, but also
the conditional probability of the amino acid to form a secondary
structure given that its immediate neighbors have already formed
that structure.

Method
The GOR method analyzes sequences to predict alpha helix, beta sheet, turn,
or random coil secondary structure at each position based on 17-amino-acid sequence
windows. The uses four scoring matrices of size 1720, where the columns
correspond to the log-odds score, which reflects the probability of finding a given
amino acid at each position in the 17-residue sequence. The four matrices reflect the
probabilities of the central, ninth amino acid being in a helical, sheet, turn, or coil
conformation.
Procedure:
1. Make 4 tables of directional information measure of helix, sheet, coil and turn i.e. GOR
Parameters (derived probability parameters of each amino acid residue to exist in helix,
sheet, coil and turn).
2. Save the tables by name dim_helix, dim_sheet, dim_coil and dim_turn
3. Run Matlab
4. Write the program.
5. Run the program formed to find the structure.
6. Analyse the result.

Program:
seq=
'gly,ala,val,leu,ile,ser,thr,cys,pro,phe,tyr,trp,his,asp,asn,glu,gln,met,lys,a
rg';
dim_helix
s1=
[gly(1)+ala(2)+val(3)+leu(4)+ile(4)+ser(6)+thr(7)+cys(8)+pro(9)+phe(10)+tyr(11
)+trp(12)+his(13)+asp(14)+asn(15)+glu(16)+gln(17)];
dim_sheet
s2=
[gly(1)+ala(2)+val(3)+leu(4)+ile(4)+ser(6)+thr(7)+cys(8)+pro(9)+phe(10)+tyr(11
)+trp(12)+his(13)+asp(14)+asn(15)+glu(16)+gln(17)];
dim_turn
s3=
[gly(1)+ala(2)+val(3)+leu(4)+ile(4)+ser(6)+thr(7)+cys(8)+pro(9)+phe(10)+tyr(11
)+trp(12)+his(13)+asp(14)+asn(15)+glu(16)+gln(17)];
dim_coil
s4=
[gly(1)+ala(2)+val(3)+leu(4)+ile(4)+ser(6)+thr(7)+cys(8)+pro(9)+phe(10)+tyr(11
)+trp(12)+his(13)+asp(14)+asn(15)+glu(16)+gln(17)];
if (s1>s2 && s1>s3&& s1>s4)
proline_predicted_structure = 'helix'
elseif (s2>s1 && s2>s3&& s2>s4)
proline_predicted_structure = 'sheet'
elseif (s3>s1 && s3>s2&& s3>s4)
proline_predicted_structure = 'turns'
else
proline_predicted_structure ='coil'
end

Required Results:
1. The program should be written
2. The program should be successfully executed.
3. It should be able to predict the structure correctly.
Output:
proline_predicted_structure

turns
Learning outcomes: