Goals for this session:
- Connect what you have observed with sequence alignments and trees to protein structures.
- Map a sequence alignment on a structure
- Interpret the results — Where are the rapidly changing residues? Where are the slowly changing residues located?
Specifically:
Tools:
-
Protein Data Bank (PDB)
National Center for Biotechnology Information (NCBI)
Biology Workbench
Consurf Server
Project:
- In groups – continue working either with the alignments you made yesterday (requires at least 6 sequences) for which a protein structure exists – or search the PDB for your favorite protein and use it to view a preformed multiple sequence alignment (MSA) from Consurf.
Post (to either the blog or project page) a report including:
- A brief intro to your protein
- Bibliographic reference
- Species used in the alignment
- An image
- Your interpretation of the results
- To questions you are still working on
