BIF501 - Bioinformatics II Handout

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Bioinformatics-II (BIF501)
Assignment No.01
Total Marks 25
Note: There is a question with multiple steps. Each step carries equal marks. Please note that every step is the pre-requisite of the following steps so you cannot leave any step. You are supposed to do your assignment by yourself. Any kind of plagiarism will be marked straight zero. Screenshot of every step should be attached in solution file.
Question 1:

1. Select a protein of your choice and also write that why you selected that protein.
2. Go to Protein databank server and download the structure of that protein.
3. Find any disease causing mutation in amino acid sequence of that particular protein. (You have to find it from literature).
4. Manually add that mutation in the protein (amino acid) sequence by replacing the normal amino acid with mutant amino acid at that position and save a separate sequence file “Protein-name_mutation”.
5. Go to FoldX server and build the mutant structure from mutant sequence. (FoldX is a Linux based tool so you have to install Linux OS on your system/PC/Laptop or you can ask your nearby VUP campuses to provide you the particular facility. Those who cannot use FoldX, are required to use Chimera/Pymol for this purpose.
6. Refine both structures.
7. Go to PROSESS web-based tool (http://www.prosess.ca/ ) and evaluate the structure.
8. Highlight the structural change at that particular position where you pointed the mutation. This could be done using PyMol.
   Note: No online tools for structure visualization will be accepted.

In case of any query please email at bif501@vu.edu.pk or contact me on Skype mjhasnain_1 before the deadline (December 12, 2019). Please note that you are given with almost 6 weeks. So, no extra time will be granted. You are supposed to do your assignment before the deadline to avoid several issues like unavailability of internet, electricity and signals etc.

Note: You will suffer in case of any Duplication/ Plagiarism.

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Ideas Solution BIF501_Assignemt_01_Sloution_Fall_2019.pdf