Reference no: EM133330500

Homology Modeling using MODELLER

Generate a structural model for the following target sequence:

GSMEKVPGEMEIERRERSEELSEAERKAVQAMWARLYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSPQL

RKHACRVMGALNTVVENLHDPDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVVAEEFASDFPPETQRAWAKLRGLI

YSHVTAAYKEVGWVQQVPNATTPPATLPSSGP

Use BLASTP to look for sequences with known structures (in the PDB) for proteins in sperm whale (taxid: 9755).

Select the best template structure, keeping in mind that % identity, E-value, and resolution are the primary criteria for judging the best initial template to use.

One important note: be careful in the PDB IDs of some proteins-in particular, the letter O and the number 0 (zero) can be easily confused, and unfortunately some PDB IDs contain both numbers and letters. It is best to copy/paste these PDB IDs so that you don't make any mistake in identifying your templates.

After generating 10 models using MODELLER, select the best model using the DOPE score as criteria.

Load the best model onto VMD, and then compare this model with the actual structure associated with the sequence above. This actual structure has the PDB ID of 3AG0 (the last digit is the number zero, not the letter O). Using VMD, compute the RMSD between the best model from MODELLER and the actual structure of 3AG0.

Take a screen shot of every step you've taken and put them in sequence below. Add descriptions to make this as detailed as possible. It will help you prepare for the hands-on part of the exam.