Lecture times:

MWF 11–12:10 PSB 305

Instructor:

Kevin Karplus (karplus@soe.ucsc.edu)

Phone: +1-831-459-4250

Office: PSB 318

Office hours: TBA (not Tuesdays)

I will have one open office hour each week, plus a regularly scheduled meeting with each student enrolled in 220L for 20-30 minutes a week (mainly to discuss the project, but homework, research, and other topics are also expected).

Students in the class this quarter:

Rachel Bingham home page

Kwok Fai Chan no home page?

Jeff Ferguson no home page?

Michael Cusack no home page?

I'll try keeping a more detailed schedule, with the topics and pointers to material to read.

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. (Kevin likes 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 have a poster session during exam week in place of a final exam. All students are expected to present a poster.

Prerequisites:

The only official prerequisite for grad students in this course is either BME 205 (bioinformatics) or CHEM 200B (protein structure), though it is best to have both. Students lacking BME 205 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 205, BIOC 100A, and CMPS 101.

Evaluation:

Roughly 40% of the evaluation will be based on the class project, 20% on in-class presentation of a journal article, 30% on homework, and 10% on general participation in class discussions (including reading most of the presented journal articles). These percentages may need to be adjusted somewhat for students doing mini-projects or for students who do multiple journal-club presentations.

Computers:

Students will be using the computers set up for bioinformatics grad students in PSB. Students can get keys for the doors at the SoE facilities office (Baskin 399C) MTWTF 1–3. The office will have a list of students in the class. School of Engineering accounts are obtained by filling out the , getting my signature on it, and turning it in to the Techstaff office. (Bioinformatics grad students already have keys and accounts.)

WWW resources for biosequence analysis

URLs for web sites containing biosequence analysis tools, but not well annotated. This is Kevin's 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. Disclaimer: Kevin is on the Board of Directors for ISCB.

SoE home

Kevin Karplus's home page

Biomolecular Engineering Department

BME 220 home page

Karplus's lab page

UCSC Bioinformatics research

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