Patrice Koehl
Department of Computer Science
Genome Center
Room 4319, Genome Center, GBSF
451 East Health Sciences Drive
University of California
Davis, CA 95616
Phone: (530) 754 5121

Computational Structural Bioinformatics: Winter 2024


General notes regarding the projects:
  • Projects are team work, with a team containing 1 or 2 (preferred) members. All members of a team will get the same grade.
  • There will be three projects, all involving some programming. You will do all 3 projects.
  • The projects will be based on many resources available on the web. It is very important that web pages, servers, research papers, textbooks, etc. used for the projects are cited properly in a reference section in the reports. I will not tolerate plagiarism of any kind.
  • Our TA put together a document on how to write an effective report for any of the projects! Please read it (available HERE)
  • See bottom of the page for main rubrics that will be used for grading the projects
Number Due date Task Documents Additional informations
1 January 25th, 2024 Introduction to the PDB database and to PyMol Handout: Word document
PDF document
2 February 13th, 2024 Viruses and diseases Handout: Word document
PDF document
3 February 29th, 2024 AlphaFold Handout: Word document
PDF document

Grading rubrics

Each project will be graded over a total of 100 points (+ 5 possible extra credit points), with the following rubrics in mind:

Rubric Name Breakdown
1 Program (total 20 pts) The following elements will be considered when grading the program:
  • Correctness: 10 points
  • Usability (input / output): 5 points
  • Clarity - comments: 5 points
2 Report (total 80 pts) The following elements will be considered when grading the report:
  • Introduction (10 points):
    • Presentation of the problem: 5 points
    • Previous work on the topic: 5 points
  • Results (60 points):
    • Presentation: 50 points
    • Analysis: 10 points
  • Discussion (10 points):
3 Beyond the prompt (total 5 pts) As mentioned in class, I will look for an analysis that goes beyond the prompt. The following elements will be considered:
  • Originality :
  • Correctness

Note: the reports are expected to be up to 5 pages long (with your choice of font / format). A report that will be more than 7 pages, will be penalized (- 5 points / page).

  Page last modified 27 February 2024