Part II: Ab initio structure prediction and Rosetta

Please use the following website to answer questions about Rosetta:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850155/

1. What is Rosetta?

2. Who is David Baker and where is his lab

3. What is Rosetta?

4. How many energy functions are used in the Rosetta ab initio structure prediction

algorithm?

5. For atomistic refinement, what are the methods for rebuilding loops supported by

Rosetta?

6. What is a rotamer and what are they useful for?

7. What sort of strategy does Rosetta take for comparative modeling?

8. Name and describe three other tools (apart from structure prediction) that can be

performed with the Rosetta software.

9. What are some important caveats to keep in mind when using Rosetta to model

proteins?

10. What is the Rosetta Commons and what do they do (http://www.rosettacommons.org)