ECS 289L

Computational Structural Biology

Protein Structure Modeling

Instructor: Patrice Koehl e-mail: koehl@cs.ucdavis.edu Web page: www.cs.ucdavis.edu/~koehl


Assignments


General notes regarding assignments:
  • Each student is allowed 2 late days to use during the quarter when submitting the assignments and/or final project. You can use them one at a time, or all at once, but once they are gone, further late assignments will be penalized (-10% per day).
  • The assignments will be based on many resources available on the web. It is very important that web pages, servers, research papers, textbooks, etc. used for assignments and the final project are cited properly in a reference section. I will not tolerate plagiarism of any kind.
  • Assignments are given in DOC or PDF format. In return, you have the choice of format to hand out your documents:
    • Paper copy is fine; you can give it to me at the end of the lecture, or in my homework box, as soon as I figure out where it is!
    • A web page containing all the results (preferred). Many Word processing programs can generate html files. If you want to program HTML yourself, there are many HTML primers on the Web. Have a look at: BareBones Guide to HTML
      Send me the URL where I can view the page, or send me an archive with the html file and all attached images...
    • A Word file or a PDF file is fine. Send them to me by e-mail
  • My e-mail address is: koehl@cs.ucdavis.edu


 
Assignment # Title Handouts Due Solutions / Notes
1 Protein Structure Visualization Word file pdf 2-1-07
2 Protein Structure Geometry Word file pdf
Coordinate file: Test.crd
Review paper: Koehl_MSRI_05.pdf
2-22-07
3 Protein Structure Prediction Word file pdf
Model1: Model1.pdb Model1.crd
Model2: Model2.pdb Model2.crd
For reference, I also add 2 files containing the energy values I obtained for the two models:
Model1: Model1.ene
Model2: Model2.ene
3-20-07
 




  Page last modified 20 February 2007 http://www.cs.ucdavis.edu/~koehl/Classes/ECS229/