CS 882: Protein Folding
Fall 2006

Ming Li DC 3355, 888-4659 mli@uwaterloo.ca

Course Information:
Course time:Mondays 4-6:30pm, DC3314.
Office hours:Drop by my office any time.
C. Branden and J. Tooze: Introduction to protein structure. 2nd edition, Garland Publishing. R.A. Friesner Ed, Computational methods for protein folding, John Wiley & Sons Inc, 2002. This book is a compilation of research papers on protein 3D prediction methods. One of our students, Bob Fraser, wrote a thesis at Queens on protein folding (with two helices). For those who look for a simple introductions, the introductory sections of his MS thesis is a good resource. More research papers on protein structure computation/prediction will be made available during the course.

Why Take This Course:

You have just missed the Genomics revolution, it has just passed. However, you have not yet missed the Proteomics revolution. It is underway, and it is impeded by a great obstacle: protein structures and functions, millions of them, are hard to determine. Unlike the genomes, which are simple storage devices for life, proteins must perform all functions for living species, hence they are very complex. Nature has spent 3 billion years to design them. Can we reveal them by computational methods? This is a very research-oriented and very focused course. We have just one objective: study all the details about protein structures, get to the bottom of it, and in the end, find a way to fold proteins accurately using computers.

Topics will include: basic biology, structural principles, motifs of protein structures, alpha-helical structures, alpha-beta structures, beta-structures, folding and flexibility, various feasible approaches for determining protein structures: X-ray, NMR, homology modeling, threading, refinement, side chain modeling, loop modeling, fragment assembly, and all sorts of energy functions.

Marking Scheme:

Each student is required to present some aspects of protein folding and is expected to do one project on a new method for protein structure determination. The class presentation will be 50% and the final project will be 50%.


No class Monday, Oct 9, 2006. The university closes because of Thanksgiving holiday!!!! We will need to reschedule another extra class time later this term.

In order to do the projects in short time, it is useful to utilize some existing resources, the following are some options. You can also explore other options on the web -- however, the bulk of your project and the main theme should be your own work.

You can download Bob Fraser's PDB file parsing program here . Thanks Bob.

You can download some classes related to protein sequence processing at BALL website as well. (This is a part of LEDA project specializing on molecular biology.)

The classroom has been changed from DC3313 to DC3314 (the next door).

Course announcements and lecture notes will appear on this page. You are responsible for reading them (and downloading the lecture notes before classes) regularly.

Lectures Notes:

Note: The lecture notes in powerpoint will gradually appear below. The lecture notes are constantly being improved, so it is a good idea to download the most recent version before class.

Projects: Xin Zhan: study of loop length, residue composition of hairpin beta motif. Yang Sun: "a detailed analysis of amino acid composition in helices (and beyond)". Bob Fraser: inference phi, psi angles given approximate C_alpha positions. Annie Lee: secondary structure/super-motif prediction. Chen Zhang: domain prediction. Babak Alipanahi: Closed barrels project. Xin Gao: refinement. Victoria Zhang: CD83 folding. Alex Xiang: Greek key motifs. Sarvagya Upadhyay: LP/Semi-definition program for hydrophobic folding. Sayyed Bashir Sadjad: conformation changes upon ligand binding. Yingying Tao: new algorithms for side chain packing positions. James Shew: Parallel beta helix (with 9 a.a. pattern)? Kunlun Tan: Prediction of open beta sheet structures.

If your name is not here yet, please send your projects to me by email.

Maintained by Ming Li, 2006