Donald developed a new Course, CS 88/188, ``Topics in Computational Molecular Biology.''
`Strictly speaking, molecular biology is not a new discipline, but rather a new way of looking at organisms as reservoirs and transmitters of information. This new vision opened up possibilities of action and intervention that were revealed during the growth of genetic engineering.'
- Michel Morange, "A History of Molecular Biology," Harvard University Press (1998).
Our goal is to look at some algorithmic problems related to three-dimensional structures in chemistry and molecular biology, emphasizing the perspective of geometric algorithms. We hope to consider a variety of topics (guided by the interests of the participants), and to make the seminar interesting to people with as wide a range of backgrounds as possible.
Some of the topics we may cover include: Protein and RNA-folding, Distance Geometry and Assignment for Protein NMR, DNA arrays, the Phase Problem in X-ray Crystallography, Rational Drug Design, Molecular Docking, identifying structural domains and motifs in proteins, and conformational search. We may read several papers on structural genomics, and papers on mass spectrometry for functional genomics.
The CS-Bio seminar is open to graduate students, and advanced undergraduates with a background in both algorithms and systems (at least CS 25 and CS 23). A background in biology is useful but not required. Students should be interested in doing some outside reading in biochemistry and biophysics. Students will be required to present papers in the seminar, and to do a project. Non-CS students (e.g., in biology and chemistry) with an interest in computational issues are invited as well.
Course is entirely on the Web.
See http://www.cs.dartmouth.edu/~brd/Teaching/.