CS 294-8 Spring 96

Computational Biology and Chemistry

TuTh 2-3:30 in 116 Calvin Lab

Course Outline for Spring 96

Note: Dan Gusfield's lectures begin Tuesday, Feb 20th

This is a new course designed to give an interdisciplinary perspective on computational problems in molecular biology and chemistry. There are many exciting possibilities for new approaches and cross-boundary collaboration. We hope to give a reasonable cross-section of the work on campus by including talks from many researchers on their specialty. The talks will be directed at an audience of non-specialists. We hope that this format highlights the common ground between researchers in different areas and departments and gives a useful overview to students starting research in one of these fields.

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.


Sung-Hou Kim, shkim@lbl.gov, 201 Hildebrand, 220 Melvin Calvin 486-4333

John Canny, jfc@cs, 529 Soda, 642-9955
The course will consist of short sequences of lectures (1-3) on particular topics. The lectures will be intended for an audience of researchers in biophysics, chemistry, physics, MCB, mathematics and computer science. A preliminary list of speakers appears below:
  • John Canny (UCB Comp Sci)
  • David Chandler (UCB Chemistry)
  • Dan Gusfield (UC Davis Comp Sci)
  • Tracy Handel (UCB MCB)
  • Theresa Head-Gordon (UCB Chemistry and LBL)
  • Martin Head-Gordon (UCB Chemistry and LBL)
  • Sung-Hou Kim (UCB Chemistry and LBL)
  • Lecture Schedule

    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)

    Useful Links

  • Journal of Computational Biology