1. What were my goals for this week?
- Get acclimated to the lab
- Finish Ken Ono's website, get that out of the way
- Read basic NMA articles, some more in-depth stuff
- Talk to Aaron and George
- Figure out classes to take in the fall
2. What did I accomplish this week?
- Finished Ono's site except for a few details to be worked out this weekend
- Read basic NMA articles, some more in-depth stuff
- Introduced self to George, had some cursory talks with Aaron and got some more resources
- Broke .xpprofile somehow; U drive doesn't mount and thus I'm stuck running IE instead of Firefox
- Talked to Greg and Aaron about fall classes, got a schedule worked out
3. Why are numbers 1 and 2 different?
Not all that different; primarily did not have as comfortable a grasp on the existing information to sit down and really pick Aaron's or George's brain. Didn't quite get Ono's site finished because of time constraints, but that should be off my shoulders by Monday so I can concentrate on research. Not sure why my .xpprofile broke; the lab has been emailed and hopefully they're figuring it out.
4. What are my goals for next week?
- Literature search for TLS
- Literature search for motion segmentation and clustering
- Get comfortable with VMD and PiMol
- Get PDBs for 3ANK and Adenylate kinase
- Go over what people are looking for when they look at motions
5. How does this fit in my bigger picture?
Getting a basic, foundational picture of the elements I will be exploring in the future, as well as just getting comfortable with the ideas I will use.
6. What did I read this week?
- Lindahl et al, NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
- Hollup et al, WEBnm@: a web application for normal mode analysis of proteins
- Wako et al, ProMode: a database of normal mode analyses on protein molecules with a full-atom model
- Kondrashov et al, Protein structural variation in computational models and crytallographic data
- Ma, Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
- Wynsberghe and Cui, Interpreting correlated motions using normal mode analysis
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