UCSC BME 200 Fall 2004
possible topics for annotated bibliography
(Last Update:
21:36 PST 3 November 2004
)
This list of possible topics was provided by David Bernick.
You can, of course, come up with your own topic.
- Protein folding progression
- History of Protein Structure determination
- The crouching dragon - a recent Nature article describing the ribosomal
tunnel, and the protein that caps the exit, protecting the unfolded protein
from proteases, while creating a pocket for domain formation.
- applications of graph theory
- How important is the initial multiple alignment to structure prediction?
- docking - building or determining a partner
- design - building function
- prions - small proteins with multiple stable conformations
- HIV proteins, HIV, or reverse transcriptases in general (error rates
maybe)
- PFAM, ProDom, CDD, ProSite, biology workbench (workbench.sdsc.edu),
Dali/FSSP, CE, .....
- Teaching
- The Pleckstrin homology domain (this would be cool for me), or SH2/SH3,
or TIM barrels, or....
- design reuse in proteins - Structure conservation across non-homologous
proteins, common domains, common functional sites. Does Nature have a short
cookbook?
Questions about page content should be directed to
Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
