Topics in Computational Molecular Biology

Computer Science 88/188
Spring, 2000

Tues, Thurs 2:00-3:50
Place: 213 Sudikoff
Professor Bruce Randall Donald
113 Sudikoff Lab, x6-3173

Overview Schedule Bibliography Some Relevant WWW Links How to give a good talk Projects


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.

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; please speak with me about your background first though.

If you took my previous CS-Bio seminar in 1998, I estimate that the papers we will read will have about 20% overlap. I plan for us to read a largely different corpus; for example, we may read several papers on structural genomics, and papers on mass spectrometry for functional genomics.

How to Give a Good Talk

If you are scheduled to give a talk, I've prepared a set of hints for giving a good talk that I encourage you to look over.


Students will be required to do a project. Pick something in the general area of computational molecular biology or algorithms for structural molecular biology you are interested in, and (a) implement it, (b) analyze it, (c) improve it, (d) extend it, or (e) apply it. A one-page written project proposal is due on May 9.

Final projects are due on the last day of class. You must

  1. Turn in a written report, and
  2. Make a web page about your project.

Recommended Textbooks

Here is a list of recommended textbooks.

Schedule and Readings

*Papers that are not available online (below) have been handed out on paper.

*RECOMB papers (Proceedings of the Nth Annual International Conference on Computational Molecular Biology (N=1,2,3,4)) are available online via the ACM Digital Library.

  • Some other papers we may read
    1. Whitepaper on Advanced Computational Structural Genomics (read the long version, not the "lite" version).
    2. Fast detection of common substructure in proteins, P. Chew, K. Kedem, J. Kleinberg, and D. Huttenlocher (RECOMB'99).
    3. Rick Lathrop Lab
    4. For Wolfson-Nussinov work on geometric hashing for protein complexes, take a look at

    Some Relevant WWW Links

  • AMMP.
  • Read the white paper on Advanced Computational Structural Genomics
  • Computational biology research at Dartmouth.
  • Check out Donald Lab Papers at
  • RECOMB'99
  • Intelligent Systems in Molecular Biology (ISMB) (all meetings).
  • Dartmouth M.D.-Ph.D. Program
  • Web sites of interest to structural biologists.
  • A large resource page on computational biology at George Mason University.
  • A large resource page on bioinformatics at the Institut Pasteur.
  • CARB Biocomputing Resources.
  • A list of protein folding groups on the web.
  • The WWW Virtual Library page on biomolecules.
  • Donald Lab.
  • The Journal of Computer-Aided Molecular Design
  • Some resources and descriptions of problems in Computational Biology.

    Related Resources on the World Wide Web

    General Notes

    Muscle-Specific Regulation of Transcription: A Catalog of Regulatory Elements by Laura L. L-pez and James W. Fickett presents a summary of published information on muscle-specific transcriptional regulation.

    Pedro's BioMolecular Research Tools is a collection of WWW links to information and services useful to molecular biologists. It provides links to molecular biology search and analysis tools; bibliographic, text, and Web search services; guides and tutorials; and biological and biochemical journals and newsletters.

    The World Wide Web Virtual Library: Biosciences points to virtual library pages for Biomolecules, and Biochemistry and Molecular Biology. Each of these pages presents a long list of Web resources. The World Wide Web Virtual Library Biomolecules covers molecular sequence and structure databases, metabolic pathway databases, and other lists of Web resources. The World Wide Web Virtual Library: Biochemistry and Molecular Biology is a list of resources listed by provider.

    Cell & Molecular Biology Online is a well-organized list of Web resources for cell and molecular biologists. For each resource, a brief description is provided.

    CSUBIOWEB, the California State University Biological Sciences Web server, provides links to other Web sites on cell biology and molecular biology.

    The Dictionary of Cell Biology (London: Academic Press, 1995) defines transcription, leucine zipper, and other terms used in this research commentary.

    Biotech Life Science Dictionary is a free resource that defines terms in biochemistry, biotechnology, botany, cell biology, and genetics, including terms used in this research commentary.

    Protein Synthesis is a tutorial on the processes involved in Protein Synthesis, starting from the genetic information in DNA, through transcription to produce messenger RNA, and translation of mRNA to a polypeptide. This tutorial is a section of Principles of Protein Structure Using the Internet, a Birkbeck College (University of London) accredited Advanced Certificate course.

    Numbered Notes

    1. Reading the Messages in Genes describes transcription and provides a diagram. This page is a unit of Access Excellence, a national educational program sponsored by Genentech that provides high school biology teachers access to their colleagues, scientists, and critical sources of new scientific information via the Web.

    2. The MIT Biology Hypertextbook is a Web-based textbook developed for introductory biology courses at MIT. Central Dogma provides an illustrated description of the process of transcription.

    3. DNA binding proteins, enhancers, and the control of gene expression describes transcription and transcription factors. This page was developed by Ronald R. D. Croy as a component of Course Notes for Molecular Genetics I Lectures.

    4. Control of Gene Expression in Eukaryotes by Phillip McClean is a tutorial on gene regulation. The Transcription Complex provides a brief discussion of transcription factors.

    5. The Mechanisms of Gene Regulation are outlined in Microbial Genetics Lecture Notes, developed by L. S. Pierson III and C. Kennedy for a class at the University of Arizona.

    6. The Wolberger Lab lists publications of Cynthia Wolberger and her co-workers.

    7. Introduction to the Metazoa describes the metazoan phyla. This introduction is a chapter of The Phylogeny of Life, an online exhibit developed by the University of California Museum of Paleontology.

    8. Protein Zippers describes the leucine zipper and provides an illustration.

    9. Barbara Graves' research is described and selected publications are listed on the Huntsman Cancer Institute Web page at the University of Utah.

    Some Useful References for the Course

    Protein Science


    Cell Biology


  • BioComputing, for the VSNS-Biocomputing Division Course
  • Biology, developed by Shane Crotty, MIT
  • Course/Tutorial on Cell Biology, Mark Dalton, Cray Research
  • Principles of Biochemistry, Horton, Moran, Ochs, Rawn, Scrimgeour

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