Literature Review and Project Proposal

It is a short report (1500 words) summarising the proposed project you are going to be doing, and discussing literature relevant to your research project. It should detail the Aim/hypothesis of the research you are going to do as well as some brief Methodology of how you will approach the project. Potential outcomes of the research should be mentioned.

Feedback on this report will be given in week 12 by your supervisor, however it is your responsibility to arrange this meeting. Feedback will be oral and written.

Interim Report

Aim of project:

To take a protein primary sequence and use it to predict the secondary and tertiary structure of protein the with a view to understanding the structure-function relationships for that protein, i.e. how the 3-D structure and functional role of the protein are related.

Protect Plan for the complete project

1. Retrieve your primary protein sequence from a protein sequence database such as UniProt

2. Investigate your protein. E.g. does the protein contain conserved domains and what are they, how does your protein interact with other proteins or drug molecules, what is its biological function?

3. Read sufficient literature to write a comprehensive introduction to your proteins function.

4. Investigate which other protein sequences are similar to your protein sequence by running BLAST (are there any matches in known 3D structures?) roe

5. Make sense of results obtained using BLAST - i.e. record E values etc for closest homologues. (Do the closest homologues have a similar biological function?).

6. What conserved domains are shared by your sequence and others found using BLAST?

7. Use Homology Modelling techniques, if appropriate, using e.g.

8. Or possibly use threading programs?

I-TASSER

9. View results obtained in graphics programs and create images of the functional regions of your protein.

10. Analyse and make sense of protein structure obtained.

11. Do protein-protein docking using CLUSPRO or protein-drug docking using SwissDock.

Programs you will be using are:

Pfam, SMART, BLASE Swiss Model, PHYRE2, I-TASSER, and graphics program such as Rasmol or Swiss PDB-Viewer.

Find the literature citations for these (not online, but paper copies) and include at end of Interim Report.