Modelling with SPDBV (Swiss PDB Viewer) or Deep View

In this example we will make a model for Ig heavy chain V region MOPC 315 [Precursor] protein.
Swiss Prot ID for this protein is P01822

Modelling through SPDBV can be done through two ways:-

  • First Approach Mode:-In this approach by pasting the amino acid sequence one can
    get the model, which can further be optimized,
    through SPDBV.
  • Optimization Mode: -This is an advanced option where we can optimize the model
    and then submit to SWISS MODEL.

So let’s begin, Save the above protein in FASTA format.

Launch SPDBV.

Open Swiss Model menu and click on Load Raw sequence to model.

The protein sequence will be visualized as a long chain of alpha helix. To submit the job you should optimize the settings.

Choose Preferences and then click on Swiss Model. Enter your name and e-mail id as the results are sent to e-mail.

As the target sequence is loaded on SPDBV, the next step is to choose templates. Open Swiss model menu and choose Find Appropriate ExPDB templates. New web page appears with sequence of target loaded on the text box. Click on Submit and wait for the results.

The server performs a BLAST search against the PDB database. Results will show the templates chosen.

Scroll down and choose PDB ID 1jptH. Save these templates by right clicking on the ID.

Open PDB File from File option. The structure with the sequence will now be visible to you

.

Click on the window menu and open the alignment window, till now both the entities are separate.

To start the fitting, click on Fit and then choose magic fit.

Now the sequence is gone but instead it has been aligned with the structure of 1jptH.You can repeatedly see both the sequence that has been aligned and the structure itself by pressing Ctrl and tab.

Now a bit of optimization can be done. Open the alignment from the window option. There you can see the alignment between two. You'll see some sign like “:” which represents exact matches, a single dot represents similar kind of amino acids while no sign represent that there is no similarity between the two at that position. You can also manually correct the alignment by using space bar and backspace.

Submission to the SWISS MODEL server.

Save it by choosing Submit modeling request from the Swiss model option and it will prompt to save the project file, a new web browser will automatically open which will tell you the path of the project file. Choose the PDB file only and submit it.

Swiss Model Submission page will appear when uploading is finished and you will get the results on e-mail.

That's all about your modelling job is done. So check your INBOX!!