Lecture times:

TTh 10-11:45 Crown 201

Instructor:

Kevin Karplus (karplus@soe.ucsc.edu)

Phone: 1-831-459-4250

Office: 315B Applied Sciences

Office hours: Tuesdays 2–3

I will have one open office hour each week, plus a regularly scheduled meeting with each student enrolled in 220L for 30 minutes a week (mainly to discuss the project, but homework, research, and other topics are also expected).

Textbooks:

There are no textbooks for BME 220 this quarter, as we will be working primarily from original literature. You may wish to have a protein-structure text such as Introduction to Protein Structure by Branden and Tooze or Protein Structure and Function by Petsko and Ringe. (I like Branden and Tooze better, but Petsko and Ringe were used for Chem 200B and for BME 220 when Carol Rohl taught it.)

If you are unfamiliar with PDB files and how protein structure is determined, I highly recommend reading Gale Rhodes's Crystallography Made Crystal Clear.

Class format:

The class will be a mixture of lectures and journal-club presentations. Evaluation will be based on participation in class discussions, on journal-club presentations, and on the term project done in BME 220L. We will most likely have a poster session during exam week in place of a final exam.

Prerequisites:

The only official prerequisite for grad students in this course is either BME 100 (bioinformatics) or CHEM 200B (protein structure), though it is best to have both. Students lacking BME 100 may need to choose a project that uses existing tools, rather than one that requires extensive programming. Students lacking CHEM 200B should have at least some knowledge of protein chemistry (at the level of BIOC 100A, for example).

For undergraduates, the prerequisites are BME 100, BIOC 100A, and CMPS 101.

Evaluation:

Roughly 40% of the evaluation will be based on the class project, 30% on in-class presentation of a journal article, 20% on homework, and 10% on general participation in class discussions (including reading most of the presented journal articles)

Other web pages of interest

WWW resources for biosequence analysis

URLs for web sites containing biosequence analysis tools, but not well annotated. This is my personal list of interesting sites, but it needs some updating, reorganizing, and annotating.

International Society for Computational Biology

ISCB is the primary professional organization for bioinformatics, sponsoring (or co-sponsoring) several conferences and having PLoS Computational Biology as its official journal. Membership pays off in reduced conference fees and journal subscriptions.

SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

Karplus's lab page

UCSC Bioinformatics research

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