Cited references and notes

1. For a wonderfully readable and informative account of the human genome, see M. Ridley, Genome, HarperCollins Publishers, New York (1999).
2. Special issue on the human genome, Science 291, No. 5507 (February 16, 2001).
3. Special issue on the human genome, Nature 409, No. 6822 (February 15, 2001).
4. IBM Journal of Research and Development 45, Nos. 3 and 4 (2001), whole issue. This issue will be available after June 2001 from IBM as G322-0227 (see ordering information on the inside back cover of the IBM Systems Journal) and viewable on the Web at http://www.research.ibm.com/journal/.
5. On the left side of the figure is a representation of DNA, obtained from http://www.mol.biol.ethz.ch/wuthrich/software/molmol/gallery.html. The relevant figure has the following caption: “Schematic picture of the DNA complex of the Antennapedia homeodomain (image done in cooperation with M. Billeter, structure solved by Y. Q. Qian et al.).” The data were rendered using the MOLMOL and POV-Ray™ visualization software. See R. Koradi, M. Billeter, and K. Wüthrich, “MOLMOL: A Program for Display and Analysis of Macromolecular Structures,” Journal of Molecular Graphics 14, 51–55 (1996). At the right end of the figure is a representation of the protein dihydrofolate reductase, viewed both without and with the ligand folate. Data for these are from the Protein Data Bank (see H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, “The Protein Data Bank,” Nucleic Acids Research 28, No. 1, 235–242 [2000]). The data are from PDB file designation “1DHF.” The primary citation is J. F. Davies II, T. J. Delcamp, N. J. Prendergast, V. A. Ashford, J. H. Freisheim, and J. Kraut, “Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate,” Biochemistry 29, No. 40, 9467–9479 (1990). The data were captured from a display rendered with the VRML plug-in for the Netscape browser. The plug-in is from Computer Associates; see www.cai.com. The plug-in allows for inclusion, or not, of the ligand bound to the protein.
6. Protein structures are archived for public use in an Internet-accessible database known as the Protein Data Bank. See http://www.rcsb.org/pdb/ and H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, “The Protein Data Bank,” Nucleic Acids Research 28, No. 1, 235–242 (2000).
7. For a highly entertaining, yet informative book that describes the exciting development of an important drug, see B. Werth, The Billion-Dollar Molecule: One Company's Quest for the Perfect Drug, Touchstone Books, Carmichael, CA (1995).
8. The Arabidopsis Genome Initiative, “Analysis of the Genome Sequence of the Flowering Plant Arabidopsis Thaliana,” Nature 408, No. 6814, 796–815 (2000).
9. See http://nar.oupjournals.org/content/vol29/issue1/#ARTICLES.
10. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic Local Alignment Search Tool,” Journal of Molecular Biology 215, 403–410 (1990).
11. Y. Duan and P. A. Kollman, “Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution,” Science 282, No. 5389, 740–744 (1998).