Protein Bioinformatics Topics
FALL 2010

Instructor: Lenore Cowen
Halligan 237; 7-5134;
Office Hours: by appointment
Lectures: Thursdays, 6:30-9pm, Halligan 106.

Rough schedule; subject to change

  • Lecture 1: September 9 (Introduction)
    (If you will need to miss the first class for religious reasons, please email me and let me know) Here is hw1
  • Lecture 2: September 16 (Protein Sequence: BLAST/Proflies/HMM) Here is hw2
  • Lecture 3: September 23 (Secondary and Super-Secondary Structure; Structure Classification; Structure alignment) Here is hw3
  • Lecture 4: September 30 (Protein Function prediction; ontologies) Here is hw4
  • Lecture 5: October 7 (Protein-protein interaction networks I) No hw this week; start thinking about project proposal!
  • Lecture 6: October 14 (Protein-protein interaction networks II) Here is hw5
  • Lecture 7: October 21 (Homology methods for structure prediction) Project proposal is due Oct 28 aim for about 3 pages plus 3 references.
  • Lecture 8: October 28 (Ab Initio protein structure prediction) Project proposal due Here is hw6
  • Lecture 9: November 4 (Docking/drug design) Here is hw7
  • November 11: Tufts closed for Veteran's day
  • Lecture 10: November 18 (Proteomics and mass spec) Here is hw8 -- this is your last hw assignment.
  • November 25: Tufts closed for Thanksgiving
  • Lecture 11: December 2 (Protein misfolding; disordered proteins) Note: class will start 1/2 hour late, at 7pm on this date!
  • Lecture 12: December 9 (Protein design) Final project due

    Description: We will look at protein bioinformatics, from sequence analysis to structure analysis and prediction, all the way to protein-protein interaction networks. This course is designed to be open both to biologists with little computational background and to computer science majors with little biology background. While little background is assumed, we will develop enough background in the course to be able to explore current research topics in the area.

    Prerequisites: Junior, Senior or Graduate Standing, or permission of the Instructor

    There is no text for this course.

    Structure of the class: Primary work in the class is a (group or individual) project. This may or may not involve our group participation in the CAFA experiment depending on the interests of students in the class.

    Additional work:

    1) If you are a graduate student, you may be asked to scribe lecture notes once during the semester. These notes are polished and handed out to the others in the class; at the end of the class there 's a beautiful set of lecture notes from these notes.

    2) "Journal club": students will be asked to read research papers and write 3 paragraph summaries.