SECONDARY STRUCTURE PREDICTION
Predicting protein tertiary structure from only its amino acid sequence is a very challenging problem, but using the simpler secondary structure definitions is more tractable.
Accurate secondary-structure prediction is a key element in the prediction of tertiary structure, in all but the simplest (homology modeling) cases.
Using the FASTA Sequence that we obtained from UniProtKB we now predict the secondary structure
of the protein we will be modelling.
Two methods were used to predict the secondary structure:
JPred
JPred is a Protein Secondary Structure Prediction server and has been in operation since approximately 1998.
JPred incorporates the Jnet algorithm in order to make more accurate predictions.
In addition to protein secondary structure JPred also makes predictions on Solvent Accessibility and Coiled-coil regions (Lupas method).
Our FASTA sequence is uploaded in the Input sequence area, and Make prediction tab is clicked to start the prediction.
The result of the predicted Jpred Secondary Structure are as follows:
From the figure we can see that helices are marked as red tubes, and sheets as green arrows. The complete set of results from the Jpred Prediction can be viewed here
GOR (Garnier-Osguthorpe-Robson) Method
The GOR method (Garnier-Osguthorpe-Robson) is an information theory-based method for the prediction of secondary structures in proteins.
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.
The protein sequence obtained in fasta format is pasted in above given link to get the below shown output.
The result from GOR are as follows:
GOR's Secondary structure prediction
Statistics of the prediction
We can see from the GOR results the percentage of helices, beta-strands and coils. Which are Alpha helix-35.56%,Extended strand - 15.11%, Random coil - 49.33%