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I590 SUPPLEMENTAL READINGS

Updated: 23 April 2006

Week 1a Introduction to Chemistry and Life Sciences Databases

Wiggins, Gary. “Overview of databases/data sources.” in Gasteiger, Johann, ed. Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes. Wiley-VCH: 2003, v. 2, pp. 496-506. http://www.indiana.edu/~cheminfo/C571/wiggins_chapter_2003.pdf

Introduction to Molecular Biology Information Resources (See the Prerequisite readings for the NLM course.)
http://www.ncbi.nlm.nih.gov/Class/MLACourse/

Nature's Horizon Symposium "Charting chemical space: finding new tools to explore biology," May 20-22, 2004.
http://www.nature.com/horizon/chemicalspace/index.html

Westerhoff, Hans V.; Palsson, Bernhard O. "The evolution of molecular biology into systems biology." Nature Biotechnology 2004, 22(10), 1249-1252. [685]

Pearson, Helen. "Biology's name game." Nature June 7, 2001, 411(6838), 631-632. [644]

Rishton, Gilbert M. "Nonleadlikeness and leadlikeness in biochemical screening." Drug Discovery Today 2003, 8, 86-96. [441]

Week 1b

STN Express with Discover! and STN on the Web; SciFinder Scholar

The Analysis Edition of STN Express with Discover!
http://www.cas.org/ONLINE/STN/discover.html

Information Retrieval: SciFinder and SciFinder Scholar
DDR02 (passim)

Schwall, Kirk; Zielenbach, Kurt. "SciFinder: A new generation of research tool." Chemical Innovation 2000 (October), 30(10), 45-50. http://pubs.acs.org/journals/chtedd/index.html

"Strategies for chemical reaction searching in SciFinder," by Damon D. Ridley J. Chem. Inf. Comput. Sci. 2000, 40, 1077-1084.
http://pubs.acs.org/journals/jcisd8/index.html

CAS SciFinder Scholar Resources http://www.cas.org/SCIFINDER/SCHOLAR/resources.html

Week 2a

Week 2b

Target Your Searching with CAS Roles (STNote No. 5)
http://info.cas.org/ONLINE/STN/STNOTES/stnotes5.pdf

CAS Roles Quick Reference Card
http://info.cas.org/ONLINE/QR/casroles.pdf

Week 3a

Week 3b

Week 4a

Searching Chemical Names

Davis, Charles H. "Nomenclature Lite:" A Guide to Naming and Indexing Chemical Compounds. http://php.indiana.edu/~davisc/Abstract.htm

Chemical Nomenclature

Week 4b

Week 5a

STRUCTURE SEARCHING

Cooke, Helen; Ridley, Damon D. "The challenges with substance databases and structure search engines." Aust. J. Chem. 2004, 57, 387-392. [650]

Dill, James D." Tautomers: involvement in searching and registration." ChemBioNews.com 2003, 13(3), 38-39. [602]

"How structure searching works," DDR96, Ch. 14.

"Searching by structure," DDR96, Ch. 15.

Week 5b

  • "Substance files with property information," DDR96, Ch. 16.

    Week 6a

    Week 6b "Using the Beilstein reaction database in an academic environment," by E. Zass. SRH98, Ch. 7.

  • "Searching for chemical reactions," DDR96, Ch. 17.

    Week 7a

    Week 7b

    Structure Searching in CAS Online Using STN Express: An Introductory Workshop

    Week 8a

    Week 8b

    Nucleic Acids Research Database issue (First issue of each calendar year)
    http://nar.oupjournals.org/content/vol34/suppl_1/

    Week 9a

    Zerhouni, Elias. "The NIH Roadmap." Science 3 October 2003, 302, 63-64, 72.

    Austin, Christopher P.; Brady, Linda S.; Insel, Thomas R.; Collins, Francis S. "NIH Molecular Libraries Initiative." Science 12 November 2004, 306, 1138-1139.

    Week 9b

    Week 10

    Week 10

    Week 11a

    Introduction to Molecular Biology Information Resources NLM course modules
    http://www.ncbi.nlm.nih.gov/Class/MLACourse/modules.html

    Week 11b

    Week 12a

    Austin, Robert. "The Complete Biosequence Patent Search: Mission Impossible?"
    http://www.stn-international.com/training_center/bioseq/piug2.pdf

    Week 12b

    Bradley, David. "Public molecules: small, but perfectly formed." Nature Reviews Drug Discovery December 1, 2004, 3, 988 doi: 10.1038/nrd1596

    Week 13a

    NLM Gateway your entrance to the knowledge resources of the National Library of Medicine

    Week 13b

    Freemantle, Michael. "Unique labels for compounds." C&EN December 2, 2002, 33-35. [535]

    Week 14a

    Week 14b

    Glusker, Jenny Pickworth; Trueblood, Kenneth N. Crystal structure analysis: a primer. 2nd ed. New York: Oxford University Press, 1985.
    QD945.G58 1985

    Week 15a

    Cambridge Structural Database

    Maginn, Steve. "World turns to Cambridge database." Bioinformatics World Jan/Feb 2002, 8-10. [433]

    Davis, Tiana V.; Zaveer, M. Shahzad; Zimmer, Marc. "Using the Cambridge Structural Database to introduce important inorganic concepts." Journal of Chemical Education 2002, 79(10), 1278-1280.

    Allen, Frank H.; Hoy, Vanessa J. "Cambridge Structural Database," in: Encyclopedia of Computational Chemistry, v. 1 pp. 155-167. (QD 39.3.E46 E53 1998 v. 1 Chemistry Reference)

    Allen, Frank H.; Kennard, Olga; Watson, David G. "Crystallographic Databases: Search and Retrieval of Information from the Cambridge Structural Database," Ch. 3 in: Structure Correlation v. 1. Ed. by Burgi, Hans-Beat and Dunitz, Jack D. Weinheim, etc., VCH, 1994 (QD461.S935 1994)

    Cambridge Crystallographic Data Centre Documentation http://www.ccdc.cam.ac.uk/support/documentation/

    Week 15b

    Week 16a

    Week 16b