BINF630/BIOL580/BINF401 Spring 2024.
Homework 2.
Due April 25, 2024.

Select a protein sequence from the table according to the last digit of your G number:

Last digit
of the G number
       
      
Protein sequence
0, 1, 2
 
SDDSQAKRVRVLELSRRLRHRGPDWSGLYQNGDNYLAHQRLAVIDPASGDQPLFNEDKTI
VVTVNGEIYNHEELRKRLKNHKFRTGSDCEVIAHLYEEYGVDFVDMLDGIFSFVLLDTRD
____________________________________________________________
3, 4, 5
 
SQEELEEGKSSLVQSLDGDWLIDYAENGQGPVNFYAEDFDDSNFKSVKVPGNLELQGFGQ
PQYVNVQYPWDGSEEIFPPQIPSKNPLASYVRYFDLDEAFWDKEVSLKFDGAATAIYVWL
____________________________________________________________
6, 7, 8, 9
 
LRANKSTSAFGLEARVPFLDKDFINTAMSLDPESKMIKPEEGRIEKWVLRRAFDDEERPY
LPKHILYRQKEQFSDGVGYSWIDGLKDHAAQNVNDKMMSNAGHIFPHNTPNTKEAYYYRM
____________________________________________________________


1. Identify the source of your sequence and the location of the fragment represented by this sequence in the protein.

2. Describe the function of this protein and it's subcellular location.

3. Check if the three-dimensional structure of your fragment is known.

4. Predict secondary structure for your sequence.

5. Find the best structural template for your sequence.
   Find the best structural template for the homology modeling of your sequence. (Corrected on 4/18/2024)

6. Predict three-dimensional structure for your sequence using homology modeling.

7. Analyze the quality of your model using one of the structure assessment tools.

8. Provide structural classification for your model.

9. Create a visualization of your model highlighting and annotating one of the important molecular or biological features.

10. FOR BINF630 AND BIOL580 STUDENTS ONLY: Compare predicted secondary structure with the secondary structure in 3D model and interpret the results.


The report should be submitted by email as a Word or PDF file with the filename "b630_24_hw2_Your_Name.doc or .pdf". The string "b630_24_hw2" should be also included in the message subject line.