UCSC BME 220 Home Page

Protein Bioinformatics, Spring 2007

(Last Update: 15:23 PDT, 21 May 2007 )

Handouts and due dates

Topics and reading list (by week---appended as the course progresses)

Intake survey---you must fill this out to get a permission code.

Project list
A project is required for BME 220L---this list gives some ideas. The only students excused from doing full-size projects are Ph.D. students who are currently do a lab rotation, or who have already finished 3 lab rotations. These students are still expected to do mini-projects. Evaluation weights for those students will be adjusted appropriately.

Grad students are urged to enter posters for their projects in the Graduate Research Symposium (Tuesday 22 May 2007, 2-4 p.m.). Undergraduates are urged to enter their projects in the Undergraduate Research Symposium (Thursday 7 June 2007).

Project proposal assignment
due 13 April 2007
The projects students actually chose will be put here.

Homework 1: drawing pictures
due 20 April 2007

The homework turned in.

Progress report due 27 April 2007. (no handout)
The progress reports should be drafts of the final report, not just "I got a lot done this week". We will provide feedback on the drafts, with suggestions for improvements in both the writing and the research. The main point of the progress reports is to teach you to write as work, and not leave it as an after-the-fact chore.

Homework 2: making a structure prediction using UCSC local tools
due 4 7 May 2007

Progress report due 11 May 2007. (no handout)
Progress report due 25 May 2007. (no handout)
Journal club presentations 30 May--8 June. We have posted a list of papers from which you may choose a paper. You may also choose a paper not on the list, but clear it with one of the instructors first. There will be 2 half-hour presentations per class, and students will get to choose papers in the order in which they are presenting (whoever goes first on 30 May has first choice of paper and so on). Signing up for presentation slots will happen on 21 May, selecting papers will happen on 23 May.

Note: a good journal club presentation not only presents the paper itself, but looks forward and back a bit: what papers did it cite? who has cited it? has the work been replaced by newer methods?

Final report due 8 June 2007. (no handout)
Poster session 12 June 2007, 4-7.

General Class Information

Lecture times:
MWF 2-3:10 PSB 305Baskin 169

Kevin Karplus (karplus@soe.ucsc.edu)
Phone: +1-831-459-4250
Office: PSB 318
Office hours: Mondays 4–5
Dietlind Gerloff (gerloff@soe.ucsc.edu)
Phone: +1-831-459-4833
Office: PSB 320
Office hours: TBA

We will each 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).

There are pictures of the students in the class in the Rogues' Gallery, to help you find out who might be able to help with homework or class projects. (Also to help Kevin remember the names of the students in the class.)

Although both professors expect to attend almost all classes, we have tentatively split the repsonsibility for the class content by weeks (we may do some trading to handle shorter or longer topics):
--- Apr 4, Kevin Apr 6, Kevin
Apr 9, Dietlind Apr 11, Dietlind Apr 13, Dietlind
Apr 16, Kevin Apr 18, Kevin Apr 20, Guest: Martin Paluszewski
Apr 23, Dietlind Apr 25, Dietlind Apr 27, Dietlind
Apr 30, Dietlind May 2, Dietlind May 4, Dietlind
May 7, Kevin May 9, Kevin May 11, Kevin
May 14, Kevin May 16, Kevin May 18, Kevin
May 21, Dietlind May 23, Dietlind May 25, Dietlind
--- May 30, students Jun 1, students
Jun 4, students Jun 6, students Jun 8, students
We are also keeping a more detailed schedule, with the topics and pointers to material to read.

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, we highly recommend reading Gale Rhodes's Crystallography Made Crystal Clear.

Class format:
The class will be a mixture of lectures and journal-club presentations, with somewhat more lecturing than in the past. 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. That poster session will be Tuesday 12 June 4-7 p.m. All students are expected to present a poster.
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.

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.
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 217) 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.)

Other web pages of interest

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: both Kevin and Dietlind are on the Board of Directors for ISCB.

slug icon to go to Scool of Engineering home page
SoE home
sketch of Kevin Karplus by Abe
Kevin Karplus's home page
Dietlind Gerloff portrait
Dietlind Gerloff's home page
BS, MS, and PhD programs
Karplus's lab page UCSC Bioinformatics research

Questions about page content should be directed to

Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064