CS298-4 will run in parallel with Chemistry 231A, a course on computational methods for chemists. Chem 231A lectures are 11:00-12:30 on Tu-Th also in 116 Calvin. Since there is significant overlap in the topics between CS298-4 and Chem 231A, there will not be a speaker in both classes every day. Instead, lectures that should be of interest to both classes will be scheduled in one slot or the other, and usually in the morning. As a general rule, the morning lectures will have an experimental/practical bias, while the afternoon lectures will deal with theoretical and algorithmic issues.
The course has been divided into "stringology" and "structural" subareas. Stringology covers biological questions on string data such as genomic sequences, protein or RNA sequences. Typical questions include genome mapping, sequence reconstruction, motif recognition, and evolutionary trees. This area has been very hot in recent years and there is an extensive arsenal of computational methods available.
The structural methods cover just about everything else. Starting from quantum chemistry, we move up the ladder to molecular dynamics, thermodynamic estimation, energy minimization, crystallographic structure, NMR, motif recognition, structure prediction from sequence data, docking, and ab initio design. The structural field is much more in flux than sequence analysis. In many cases, there is no clear choice of model for the physical system. Gross approximations are often needed because of computational limits, and then the usefulness of the predictions must be examined very carefully. The modeling problem therefore is an important and recurring theme in structural methods.
Date Chem 231 A Speaker CS 298-4 Speaker 11-12:30 in 116 Calvin 2-3:30 in 116 Calvin 2/6/96 ---------- John Canny (C298-4 Intro.) 2/8/96 Manfred Zorn, LBL ---------- (Sequence Homology) 2/13/96 Manfred Zorn, LBL ---------- (Open-Reading Frames) 2/15/96 Manfred Zorn, LBL ---------- (Sequence Databases) 2/20/96 Barbara Bowman Dan Gusfield, UCD (Phylogenetic Analysis) (multiple alignments) 2/22/96 Steve Holbrook, LBL Dan Gusfield, UCD (secondary structure pred.) (Suffix trees) 2/27/96 Steve Holbrook, LBL (secondary structure pred.) 2/29/96 Sung-Hou Kim, LBL & UCB ---------- (tertiary structure pred.) 3/5/96 Sung-Hou Kim, LBL & UCB ---------- (tertiary structure pred.) 3/5/96 Ken Dill, UCSF ---------- (Models of Protein folding) 3/7/96 Paul Gordon ---------- (Docking and Drug Design) 3/12/96 ---------- No lecture 3/14/96 ---------- No lecture 3/19/96 ---------- John Canny, UCB (Docking Algorithms) 3/21/96 ---------- John Canny, UCB (Geometric Hashing) 4/2/96 Theresa Head-Gordon ---------- (Thermodynamic estimation) 4/4/96 Theresa Head-Gordon ---------- (Thermodynamic estimation) 4/9/96 David Wemmer (structure from NMR) 4/11/96 Sung-Hou Kim, LBL & UCB (Assessment of crystal structure)