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C371 Chemical Informatics I SUPPLEMENTAL READINGS

Updated: 13 October 2003

0. Introduction to Chemical Informatics

Stapleton, Michael. "Informatics Meets the Chemical Enterprise." Chemical & Engineering News. March 26, 2001, 283.
http://pubs.acs.org/cen/index.html (available only to ACS members online: IU and IUPUI Libraries do not have a subscription to the online version)


I. Representation and Manipulation of 2D Molecular Structures

Leach & Gillet, chapter 1

II. Representation and Manipulation of 3D Molecular Structures

Leach & Gillet, chapter 2

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 Library 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)

The CSD System Documentation http://www.ccdc.cam.ac.uk/support/csd_doc/zdocmain.html

III. Molecular Descriptors

Leach & Gillet, chapter 3

Ertl, Peter; Jacob, Olivier. "WWW-Based Chemical Information System." http://www.elsevier.com/inca/homepage/saa/eccc3/paper6/

IV. Computational Models

Leach & Gillet, chapter 4

V. Similarity Methods

Leach & Gillet, chapter 5

VI. Selecting Diverse Sets of Compounds

Leach & Gillet, chapter 6

VII. Analysis of High-Throughput Screening Data

Leach & Gillet, chapter 7

VIII. Virtual Screening

Leach & Gillet, chapter 8

Lesney, Mark S. "Gearing Up for Speedy Relief." Today's Chemist at Work. January 2003, 22-24; 27. http://pubs.acs.org/subscribe/journals/tcaw/12/i01/toc/toc_i01.html

IX. Combinatorial Chemistry and Library Design

Leach & Gillet, chapter 9

Molecular Codes

Brecher, J. "Name= Struct: A Practical Approach to the Sorry State of Real-Life Chemical Nomenclature." J. Chem. Inf. Comput. Sci. 1999, 39, 943-950.
http://pubs.acs.org/journals/jcisd8/index.html


Barta, Nancy S.; Stille, John R. "Grasping the Concepts of Stereochemistry." J. Chem. Educ. 1994, 71(1), 20-23.


Baumgras, Jan L.; Rogers, Anne E. "Chemical Structures at the Desktop: Integrating Drawing Tools with On-Line Registry Files." J. Amer. Soc. Info. Sci. 1995, 46(8), 623--631.


Molecular Visualization

Lesk, Michael. "Going Digital." Scientific American March 1997, 276(3), 58-60.
http://www.sciamarchive.org/

Marcey, David J. "Molecular Visualization for the Masses." (WebScan) HMS Beagle, The BioMedNet Magazine Issue 90, November 10, 2000. http://news.bmn.com/hmsbeagle

Driscoll, Timothy. RasMol 2.7 (Software Review) HMS Beagle, The BioMedNet Magazine Issue 109, August 31 - September 13, 2001 HMS Beagle, The BioMedNet Magazine Issue 109, August 31 - September 13, 2001
http://news.bmn.com/hmsbeagle

Rhodes, Gail. Introduction to Molecular Modeling: A Tutorial for RasMol.
http://www.usm.maine.edu/~rhodes/RasTut/index.html

Eliopoulos, E.; Mavridis, I.M. MAGE Tutorial: An Interactive-Kinetic Approach to the Study of Supramolecular Structures. (diskette included with: Crystallography of Supramolecular Compounds. Dordrecht: Kluwer, 1996) QD381.9 .S87 C79 1996

Simon, Hank. "Scalabale Vector Graphics." Today's Chemist at Work 2002, 11(6): 17-20. http://pubs.acs.org/subscribe/journals/tcaw/11/i06/html/06comp.html

XML/CML references

Davies, Antony N. "XML in Chemistry." Chemistry International. July 2002, Vol. 24, 4, 3-8.


Murray-Rust, Peter; Rzepa, Henry S. "Markup Languages--How to Structure Chemistry-Related Documents." Chemistry International. July 2002, Vol. 24, 4, 9-13.  article


Bradley, David. "The Chemical Brotherhood." Scientific Computing World. July/August 2002, 65, 9-10. article


Joyce, John. "XML." (SC&I Online Scientist). Scientific Computing & Instrumentation June 2000, 10.
www.scimag.com

Ray, Erik T. Learning XML. Sebastopol, CA: O'Reilly, 2001.

Murray-Rust, Peter; Rzepa, Henry S. "Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles." J. Chem. Inf. Comput. Sci. 1999, 39, 928-942.
http://pubs.acs.org/journals/jcisd8/index.html

Murray-Rust, Peter; Rzepa, Henry S. "Chemical Markup, XML, and the Worldwide Web. 2. Information Objects and the CMLDOM." J. Chem. Inf. Comput. Sci. 2001, 41, 1113-1123.
http://pubs.acs.org/journals/jcisd8/index.html

Gkoutos, Georgios V.; Murray-Rust, Peter; Rzepa, Henry S. "Chemical Markup, XML, and the Worldwide Web. 3. Toward a Signed Semantic Chemical Web of Trust." J. Chem. Inf. Comput. Sci. 2001, 41, 1124-1130.
http://pubs.acs.org/journals/jcisd8/index.html

Wright, Michael; Rzepa, Henry S.; Zara, S.; Murray-Rust, Peter. "Development of a Chemical Markup Language (CML) as a System for Handling Complex Chemical Content."
http://www.chemsoc.org/exemplarchem/entries/wright/writeup.xml


Electronic Publishing

Notess, Greg. "Browser Diversity." Online 2001, 25(4), 66-68.


Heller, Steven R. "Electronic Publishing of Scientific Manuscripts", In: Encyclopedia of Computational Chemistry, Schleyer, P. von R.; Allinger, N.L.; Clark, T.; Gasteiger, J.; Kollman, P.A.; Schaefer, H.F.; Shreiner, P.R. (Eds.). Wiley, Chichester, 2, 871-875.
QD39.3.E46 E53 1998


May, P.W. "The Visualisation of Chemical Processes for Electronic Publishing and Presentations." PhysChemCom 2001, 17. (DOI: 10.1039/b103982m;
Free version: http://xlink.rsc.org/?DOI=10.1039/b103982m


Gkoutos, G.V.; Rzepa, H.S. "A Mechanism for Creating Chemically Oriented Internet Search Channels." Internet Journal of Chemistry 2000, 3 (Article 8).
http://www.ijc.com/


Beit-Arie, Oren et al. "Linking to the Appropriate Copy." D-Lib Magazine September 2001, 7(9).
http://www.dlib.org/dlib/september01/caplan/09caplan.html


Using Chemical Data

Hall, Sydney R.; Allen, Frank H.; Brown, I. David. "The Crystallographic Information File (CIF): A New Standard Archive File for Crystallography." Acta Crystallogr., Sect. A: Found. Crystallogr. 1991, A47(6), 655-685.

Dalby, Arthur et al. "Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited." J. Chem. Inf. Comput. Sci. 1992, 32, 244-255.

Kling, Jim. "Tearing Down the Tower of Babel: First steps toward a common language for analytical data." Anal. Chem. September 1999, 621A-623A. http://pubs.acs.org/isubscribe/journals/ancham-a/71/i17/html/focus.html




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