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I647 SUPPLEMENTAL READINGS

Updated: 16 November 2006
Week 1 Introduction to PubChem, the NIH Roadmap Program, and the CICC

Bradley, David. "Public molecules: small, but perfectly formed." Nature Reviews Drug Discovery December 1, 2004, 3, 988.
DOI: 10.1038/nrd1596 [686]

Brown F. "Editorial opinion: chemoinformatics - a ten year update." Current Opinion in Drug Discovery and Development 2005 May; 8(3): 298-302.
pdf [812]

Curcin, Vera; Ghanem, Moustafa; Guo, Yike. "Web services in the life sciences." Drug Discovery Today 2005, 10(12), 865-871.
pdf [731]

Tetko, Igor V. "Computing chemistry on the web." Drug Discovery Today November 15, 2005, 10(22), 1497-1500.
pdf [795]

Sild, Sulev; Maran, Uko; Lomaka, Andre; Karelson, Mati. "Open Computing Grid for Molecular Science and Engineering." Journal of Chemical Information and Modeling 2006, 46(3), 953-959.
DOI: 10.1021/ci050354f [754]

Nucleic Acids Research

Week 2 Bridging Bioinformatics and Chemical Informatics

"The Bigger Picture: Linking Bioinformatics to Cheminformatics" [CINF Symposium] Abstracts [1-16], 227th ACS National Meeting Anaheim, CA, March 28-April 1, 2004
http://www.acscinf.org/docs/meetings/227nm/227cinfabstracts.htm

Intergrative Informatics PowerPoint by John Reynders (Lilly) for David Wild's I590 course, Spring 2006

Austin, C.P. "The completed human genome: implications for chemical biology." Current Opinion in Chemical Biology 2003, 7(4), 511-515.
pdf [810]

Jorgensen, William L. "The many roles of computation in drug discovery." Science March 19, 2004, 303, 1813-1818.
pdf [815]

Nature's Horizon Symposium "Charting chemical space: finding new tools to explore biology," May 20-22, 2004. (See the Background, Key Questions, and Symposium Highlights sections.)
http://www.nature.com/horizon/chemicalspace/index.html

Povolna, Vera; Dixon, Scott; Weininger, David. "Cabinet-Chemical and Biological Informatics NETwork." in: Oprea, Tudor I., ed. Chemoinformatics in Drug Discovery. Weinheim: Wiley-VCH, 2004, 241-269.

Week 3 Knowledge Discovery and Data Mining in Chemistry

Kalos, Alex; Rey, Tim. "Data mining in the chemical industry." KDD '05, August 21-25, 2005, Chicago, IL, USA. 2004 ACM 1-58113-000-0/00/0004
pdf [821]

Taylor, K. R.; Gledhill, R. J.; Essex, J. W.; Frey, J. G. "Bringing chemical data onto the semantic web." Journal of Chemical Information and Modeling 2006, 46, 939-952.
DOI: 10.1021/ci050378m [749]

Banville, Debra L. "Mining chemical structural information from the drug literature." Drug Discovery Today January 2006, 11(1/2), 35-42.
pdf [855]

Agresti, William W. "Discovery informatics." Communications of the ACM August 2003, 46(8), 25-28.
pdf [ 851]

Bajcsy, Peter; Han, Jiawei; Liu, Lei; Yang, Jiong. "Survey of biodata analysis from a data mining perspective." Chapter 2 in: Wang, Jason T.L.; Zaki, Mohammed J.; Toivonen, Hannu T. T.; Shasha, Dennis, eds. Data Mining in Bioinformatics. N.Y.: Springer Verlag, 2004, pp. 9-39.
pdf [849]

Week 4 High Throughput Screening

Troyanskaya, Olga G. "Putting microarrays in a context: Integrated analysis of diverse biological data." Briefings in Bioinformatics Mar2005, 6(1), 34-43.
pdf [853]

Week 5 Virtual Screening

Irwin, J.J.; Shoichet, B.K. "ZINC-A free database of commercially available compounds for virtual screening." Journal of Chemical Information and Modeling 2005, 45, 177-182.
pdf [703]

Week 6 Open Source Chemistry Tools

Geldenhuys, W.J.; Gaasch, K.E.; Watson, M.; Allen, D.D.;Van Der Schyf, C.J. "Optimizing the use of open-source software applications in drug discovery." Drug Discovery Today February 2006, 11(3/4), 127-132.
pdf [814]

Papers from "Web-Based Applications for Chemical Education: Experiences and Visions," an on-line conference, beginning May 5, 2006.
http://www.stolaf.edu/depts/chemistry/bh/confchem/confchem_s2006.htm

Week 7 The Chemical Semantic Web

Coles, Simon J.; Day, Nick E.; Murray-Rust, Peter; Rzepa, Henry S.; Zhang, Yong . "Enhancement of the chemical semantic web through the use of InChI Identifier s." Organic & Biomolecular Chemistry 2005, 3, 1832-1834.
pdf [736]

Guha, R.; Howard, M.T.; Hutchison, G.R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C; Wegner, J.; Willighagen, E.L. "The Blue Obelisk-Interoperability in chemical informatics." Journal of Chemical Information and Modeling 2006 Web Release Date: 22-Feb-2006.
DOI: 10.1021/ci050400b
pdf [854]

Murray-Rust, Peter S.; Mitchell, John B.O.; Rzepa, Henry S. "Communication and re-use of chemical information in bioscience." BMC Bioinformatics 2005, 6, 180.
DOI: 10.1186/1471-2105-6-18 0
pdf [735]

Murray-Rust, Peter; Mitchell, John B.O.; Rzepa, Henry S. "Chemistry in bioinformatics." BMC Bioinformatics 2005, 6, 141-144.
pdf [737]

Introduction to the Semantic Web (Ivan Herman, W3C, 5/24/2006)

Week 8 Chemical Databases

Jónsdóttir, S.O.; Jorgensen, F.S.; Brunak, S. "Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates." Bioinformatics 2005 May 15; 21(10): 2145-60.
pdf [859]

Kekota, Justin; Roth, Frederick P.; Schreiber, Stuart L. "Query Chem: A Google- powered web search combining text and chemical structures." Bioinformatics 2006, 22(13), 1670-1673.
http://bioinformatics.oxfordjournals.org/cgi/reprint/22/13/1670

Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey, Jennifer. "DrugBank: a comprehensive resource for in silico drug discovery and exploration." Nucleic Acids Res. 2006 Jan 1;34(Database issue): D668-72.
pdf [808]

Chen, Jonathan; Swamidass, S. Joshua; Dou, Yimeng; Bruand, Jocelyne; Baldi, Pierre. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics 2005, 21(22), 4133-4139.
pdf [758]

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

Dunkel, M.; Fullbeck, M.; Neumann, S.; Preissner, R. "SuperNatural: a searchable database of available natural compounds." Nucleic Acids Research 2006, 34, Database issue D678-D683.
DOI:10.1093/nar/gkj132 [798]

Roter, A.H. "Large-scale integrated databases supporting drug discovery," Current Opinion in Drug Discovery & Development 2005 (May), 8(3), 309-315.
pdf

Weeks 9-10 Life Science Databases

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

Nucleic Acids Research

Andreeva, A.; Howorth, D.; Brenner, S.E.; Hubbard, T.J.P.; Chothia, C.; Murzin, A.G. "SCOP database in 2004: refinements integrate structure and sequence family data." Nucleic Acids Research 2004, 32 Database issue D226-D229.
DOI: 10.1093/nar/gkh039 [797]

Gold, Nicola D.; Jackson, Richard M. "A searchable database for comparing protein-ligand binding site for the analysis of structure-function relationships." Journal of Chemical Information and Modeling 2006, 46(2), 736-742.
pdf [791]

Kanehisa, M.; Goto, S.; Hattori, M.; Aoki-Kinoshita, F. Itoh, M.; Kawashima, S.; Katayama, T.; Araki, M; Hirakawa, M. "From genomics to chemical genomics: new developments in KEGG." Nucleic Acids Research 2006, 34, Database issue D354-D357.
DOI: 10.1093/nar/gkj102 [801]

Kellenberger, Esther; Muller, Pascal; Schalon, Clarire; Bret, Guillaume; Foata, Nicolas; Rognan, Didier. "sc-PDB: An annotated database of druggable binding sites from the Protein Data Bank." Journal of Chemical Information and Modeling 2006, 46(2), 717-727.
pdf [790]

Kouranov, A.; Xie, L. de la Cruz, J.; Chen, L.; Westbrook, J.; Bourne, P.E.; Berman, H.M. "The RCSB PDB information portal for structural genomics." Nucleic Acids Research 2006, 34, Database issue D302-D305
DOI: 10.1093/nar/gkj120 [802]

Kumar, M.D.S.; Gromiha, M.M. "PINT: Protein-protein interactions thermodynamic database." Nucleic Acids Research 2006, 34 Database issue D195-D198.
DOI: 10.1093/nar/gkj017 [803]

Lo Conte, L.; Brenner, S.E.; Hubbard, T.J.P.; Chothia, C.; Murzin, A.G. "SCOP database in 2002: refinements accommodate structural genomics." Nucleic Acids Research 2002, 30(1): 264-267.
pdf [804]

Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C. "SCOP: A structural classification of proteins database for the investigation of sequences and structures." Journal of Molecular Biology 1995, 247, 536-540.
pdf [806]

Okuno, Y.; Yang, J.; Taneishi, K.; Yabuuchi, H.; Tsujimoto, G. "GLIDA: GPCR-ligand database for chemical genomic drug discovery." Nucleic Acids Research 2006, 34, Database issue D673-D677.
DOI: 10.1093/nar/gkj028 [807]

Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis." Nucleic Acids Research. 2005, 33 Database Issue D247-D251.
pdf

Stoeckert, C.J. "Functional genomics databases on the web." Cellular Microbiology 2005 (August), 7(8), 1053-1059.
pdf

van Beek, Johannes H.G.M. "Channeling the data flood: Handling large-scale biomolecular measurements in silico." Proceedings of the IEEE, April 2006, 94(4), 692-709.
TK5700 .I6 Swain Hall Library

Wheeler, D.L. et al. "Database resources of the National Center for Biotechnology Information." Nucleic Acids Research 2006, 34 Database Issue D173-D180. DOI: 10.1093/nar/gkj158 [809]

Week 11 Ontologies and Vocabulary Control

Feldman, H.J.; Dumontier, M.; Ling, S. et al. "CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules." FEBS LETT 579 (21): 4685-4691 AUG 29 2005
pdf

Gardner, S.P. "Ontologies and semantic data integration." Drug Discovery Today 2005 (July 15), 10(14), 1001-1007.
pdf [734]

Pearson, Helen. "Biology's name game." Nature June 7, 2001, 411(6838), 631-632.
DOI: 10.1038/35079694
pdf [644]

Week 12 Text Mining

Cohen, Aaron Michael; Hersh, William R. "A survey of current work in biomedical text mining." Briefings in Bioinformatics March 2005, 6(1), 57-71.
pdf [850]

Zimmermann, Marc; Fluck, Juliane; Thi, Le Thuy Bui; Kolarik, Corinna; Kumpf, Kai; Hofmann, Martin. "Information extraction in the life sciences: Perspectives for medicinal, chemistry, pharmacology and toxicology." Current Topics in Medicinal Chemistry 2005, 5(8), 785-796.
Abstract

Zimmermann, Marc; Thi, Le Thuy Bui; Hofmann, Martin. "Combating illiteracy in chemistry: Towards computer-based chemical structure reconstruction." ERCIM News January 2005, 60, 40-41.
pdf

A Compendium of Free, Public Biomedical Text Mining Tools Available on the Web

Week 14 Pharmacogenomics

Yan, Qing. "Biomedical informatics methods in pharmacogenomics." Methods in Molecular Medicine 2005, 108 (Hypertension), 459-486.
Abstract

Vyas, H.; Summers, R. "An information-driven approach to pharmacogenomics." Pharmacogenomics 2005 (July), 6(5), 473-480.

Burren, Oliver S.; Healy, Barry C.; Lam, Alex C.; Schuilenburg, Helen; Dolman, Geoffrey E.; Everett, Vincent H.; Laneri, Davide; Nutland, Sarah; Rance, Helen E.; Payne, Felicity; Smyth, Deborah; Lowe, Chris; Barratt, Bryan J.; Twells, Rebecca C. J.; Rainbow, Daniel B.; Wicker, Linda S.; Todd, John A.; Walker, Neil M.; Smink, Luc J. "Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics." Human Genomics 2004, 1(2), 98-109.
Abstract

Altman, Russ B.; Klein, Teri E. "Challenges for biomedical informatics and pharmacogenomics." Annual Review of Pharmacology and Toxicology 2002, 42, 113-133.
pdf

"The contribution of molecular informatics to chemogenomics. Knowledge-based discovery of biological targets and chemical lead compounds." Jacoby, Edgar; Schuffenhauer, Ansgar; Acklin, Pierre. Methods and Principles in Medicinal Chemistry 2004, 22 (Chemogenomics in Drug Discovery), 139-166.

Week 15 Proteomics

Sheeley, D.M.; Breen, J.J.; Old, S.E. "Building integrated approaches for the proteomics of complex, dynamic systems: NIH programs in technology and infrastructure development." Journal of Proteome Research 4 (4): 1114-1122 JUL-AUG 2005.
pdf

Ahrens, Christian; Jespersen, Hans; Schandorff, Soeren. "Bioinformatics for proteomics." Methods of Biochemical Analysis 2005, 45 (Industrial Proteomics), 249-272.

Gagna CE, Winokur D, Clark Lambert W. "Cell biology, chemogenomics and chemoproteomics." Cell Biol Int. 2004; 28(11): 755-64. [813]
pdf

Souchelnytskyi, S. "Bridging proteomics and systems biology: What are the roads to be traveled?" Proteomics 2005 (November), 5(16), 4123-4137.
pdf

Creighton, Chad; Hanash, Samir M. "Informatics tools for functional pathway analysis using genomics and proteomics," In: Srivastava, Sudhir, ed. Informatics in Proteomics. CRC Press LLC, Boca Raton, Fla, 2005, 193-203.

Jurisica, Igor; Wigle, Dennis. Knowledge Discovery in Proteomics Boca Raton: Chapman & Hall/CRC, 2006.

Week 15 Glycomics

Raman, R.; Raguram, S.; Venkataraman, G.; Paulson, J.C.; Sasisekharan, R. Glycomics: an integrated systems approach to structure-function relationships of glycans." Nature Methods 2005 (November), 2(11), 817-824.
pdf

Dove, Alan. "Counting Carbs: Glycomics Gears Up ." G&P March 2006 (cover story) ,6(2), 10-14.
Full Text Link [838]

Other Readings

Schubert, Ulrich S. "Materials informatics: from data to knowledge towards integrated escience approaches." QSAR & Combinatorial Science 2005, 24(1), 5.

MacMullen, W.J.; Denn, S.O. "Information problems in molecular biology and bioinformatics." Journal of the American Society for Information Science and Technology 2005 (March), 56(5), 447-456.

Gilardoni, Francois; Curcin, Vasa; Karunanayake, Kanishka; Norgaard, Jonas; Guo, Yike. "Integrated informatics in life and materials sciences: an oxymoron?" QSAR & Combinatorial Science 2005, 24(1), 120-130.

Lange, B.M.; Ghassemian, M. "Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps." Phytochemistry 2005 (February), 66(4), 413-451.

Belkowski, S.M.; Polkovitch, D.; D'Andrea, M.R. "Synergistic approaches to clinical oncology biomarker discovery." Current Topics in Medicinal Chemistry 2005, 5(11), 1047-1051.

Ohlstein, Eliot H.; Johnson, Anthony G.; Elliott,John D.; Romanic, Anne M. New strategies in drug discovery," Methods in Molecular Biology 2005, 316, 1-11.

Cary, M.P.; Bader, G.D.; Sander, C. "Pathway information for systems biology." FEBS Letters 2005 (March 21), 579(8), Special Issue SI, 1815-1820.

Vidal, M. "Interactome modeling." FEBS Letters (March 21), 579(8), Special Issue SI, 1834-1838.

Aloy, P.; Russell, R.B. "Structure-based systems biology: a zoom lens for the cell." FEBS Letters 2005 (March 21), 579(8), Special Issue SI, 1854-1858.

Westerhoff, Hans V.; Palsson, Bernhard O. "The evolution of molecular biology into systems biology." Nature Biotechnology 2004 (October), 22(10), 1249-1252. [685] (This issue focuses on the potential applications of systems biology to biotechnology.)

Ekins, Sean, ed. Computer Applications in Pharmaceutical Research and Development. Hoboken, NJ: John Wiley & Sons, 2006.

Jaroch, S.; Weinmann, H., eds. Chemical Genomics: Small Molecule Probes to Study Cellular Function. Berlin: Springer, 2006.

Darvas, Ferenc; Guttman, Andras; Dorman, Gyorgy, eds. Chemical Genomics. New York, Dekker, 2004.

Oprea, Tudor I., ed. Chemoinformatics in Drug Discovery. Weinheim: Wiley-VCH, 2005. (Methods and Principles in Medicinal Chemistry, v. 22)

Bajorath, Jürgen, ed. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. Totowa, N.J. : Humana Press, c2004. (Methods in molecular biology ; v. 275)

Nagl, Sylvia, ed. Cancer Bioinformatics: From Therapy Design to Treatment Chichester, England; Hoboken, NJ: John Wiley & Sons, c2005.

Cheminformatics Journals and Other Publications

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