Bioinformatics Project

Session 1 - Learning about the protein sequence and investigation of protein domains.

1. Use your protein sequence reference code and get information about your protein

2. Look through the files locating the number of amino acids present and the function of your protein. Also look for any other important information.

3. Write in your lab book a reasonable amount about what you have found within the (Uniprot file)

4. Cross-links to the different Family and domain databases and ascertain the domains present within your protein and the amino acids present within those domains. (Graphical view in Smart and Pfam databases works well). Make a note of these. Do the different domain databases give similar results in terms of domains found and the amino add residues present within those domains?

5. Take a look at the protein-protein interactions of your protein and what drug it interacts with, if any.

Use a notebook to record all of your findings. This is your logbook and needs to be submitted later as an item of assessment. Therefore make sure you write up result comprehensively. Each entry made in logbook should be a dated entry.

Session 2

1. Run protein-protein BLAST for your sequence. Websites for BLAST either at NCBI or EBI.

2. Run against both a protein sequence database i.e. SWISS-PROT part of Uniprot and the protein DataBank (pdb) - 2 independent runs.

3. Either printout or save html output files.

4. Read through HELP facilities at BLAST sites and attempt to understand how to interpret the output produced.

5. Be ready to discuss output from BLAST.

Session 3

1. From your Blast search against a protein sequence database, identify those sequences with close homology. Discuss your results and your criteria for assessing sequences.

2. From Blast search against the protein data bank (PDB) identify those sequences with close homology. Which part of your sequence is homologous to already determined 3-D structures? - identify the range of amino acids within your sequence which display high homology with existing 3-D structures and report % identity.

3. Look in the Proteiri Data Bank at the homologous structures found. You will need to include a discussion of these structures with pictures and discussion of the three-dimensional structures in your Final write-up. Download information from the PDB and get hold of the citations (for at least one for each matched region).

Session 4

1. Work out an approximate % homology of your sequence with existing known crystal structures (3D structures).

2. Having ascertained that a reasonably high % of your protein sequence has homology with existing 3-D structures we will now try to do homology modeling for the entire length of the protein sequence.

3. Using your sequence information as before use the homology modelling servers Swiss-Model to find a model for your sequence.

4. Servers will produce results files which will be e-mailed to you. The pdb files contain coordinates for models produced.

5. Use Swiss PDB viewer (DeepView) for Swiss-Model output and rasmol for 3D-jigsaw (may also be able to use Swiss PDB viewer) to view output files.