Procedure:

In this exercise one can learn how to analyze the secondary structure  of a protein using SOPMA. Figure 1 shows the home page of SOPMA.

For info to retrieve the input sequences go to simulator tab.

Figure1: Home page of SOPMA

Here we can paste the computerized protein sequence in the text box provided. By default the output width is 70. It means that in the output shows up to 70 amino acids in each line. We can change the output width if we want. In the parameters there are options like ‘Number of conformational states’, ‘Similarity threshold’ and ‘Window width’. The user can select ‘Number of conformational states’ as either ‘(3Helix, Sheet, Coil)’ or ‘4(Helix, Sheet, Turn, Coil). The former predicts the percentage of helix, sheet and coil structure while the latter predicts percentage of helix, coil, turn and sheet.

Figure 6: Paste the FASTA sequence of hemoglobin. Now click on the submit button.

Following figures shows the SOPMA results.

Figure7: SOPMA results

Since the output width we set as 70, here it shows 70 amino acids and corresponding predicted structures in each line. The sequence length is also displayed in the output (333 amino acids in this case). The percentage of each structure is also listed in this page. For example, for Alpha helix it is 59.46%.

Figure 8: SOPMA results

There are two graphs shown in the result page of SOPMA. First one is to visualize the prediction. The second contains score curves for all predicted states.It also shows the parameters such as window width, number of states etc. that are used for the prediction. It provides a link on prediction result file which gives the result in a text format. There are links to find the intermediate result files also.