Module IV

3D Structure Prediction, Visualization and Evaluation

Assignment

  1. Find the protein associated with the accession number: Q53PC4 on UniProt and note its name and total sequence length of the amino acids. Does it have a structure?

  2. Why would you download its FASTA sequence & how?

  3. BLAST the sequence against PDB database to find the best template for modeling and report:

  4. What protein you selected as a template?

  5. Why did you choose it?

  6. What 3D prediction approach you think might fit best & Why?

  7. Retrieve the PDB structure of your template and predict a total of 5 structures using 2 different tools of your target protein. Provide the accession of the PDB ID that you selected as a template.

  8. Which tools did you use to predict the structure of the protein & why?

  9. What’s the overall outcome of your 3D prediction?

  10. Select the best model through evaluation on ERRAT and RAMPAGE, create an excel sheet and create a chart of your results.

  11. Visualize your models in Chimera, Color them according to their secondary structure and MatchMaker (Align) all 5 of them and export their pictures.

  12. Visualize your models in PyMol, Align them through command-line, report their RMSD value and create surface representations of your models with colors of your choice, applied on secondary structures. Report back with pictures.

  13. Put all of your questions and answers in a single .docx file and submit it.

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