Introduction to Cheminformatics
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- Abstract
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- Literature Cited
Abstract
Cheminformatics is a relatively new field of information technology that focuses on the collection, storage, analysis, and manipulation of chemical data. The chemical data of interest typically includes information on small molecule formulas, structures, properties, spectra, and activities (biological or industrial). Cheminformatics originally emerged as a vehicle to help the drug discovery and development process, however cheminformatics now plays an increasingly important role in many areas of biology, chemistry, and biochemistry. The intent of this unit is to give readers some introduction into the field of cheminformatics and to show how cheminformatics not only shares many similarities with the field of bioinformatics, but that it can also enhance much of what is currently done in bioinformatics.
Keywords: Cheminformatics; bioinformatics; chemical genomics; drug; chemical
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PDF or HTML at Wiley Online LibraryTable of Contents
- The Intersection Between Cheminformatics and Bioinformatics
- Databases in Cheminformatics
- Database Searching in Cheminformatics
- Property Prediction in Cheminformatics
- Conclusion
- Acknowledgements
- Literature Cited
- Tables
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Literature Cited
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| Key References | |
| Doucet, J‐P. and Weber, J. 1996. Computer‐Aided Molecular Design: Theory and Applications. Academic Press, London. | |
| An excellent introduction to the concepts and algorithms used in drug design and molecular modeling. This textbook covers methods and tools for both proteins and small molecule chemicals. Don't let the date be deceiving. | |
| Jonsdottir, S.O., Jorgensen, F.S., and Brunak, S. 2005. Prediction methods and databases within chemoinformatics: Emphasis on drugs and drug candidates. Bioinformatics 21:2145‐2160. | |
| A superb review, with a nice summary of both open source and commercial databases. This review also provides useful assessments and descriptions of chemical property prediction and drug metabolism software. | |
| Geldenhuys, W.J., Gaasch, K.E., Watson, M., Allen, D.D., and Van der Schyf, C.J. 2006. Optimizing the use of open‐source software applications in drug discovery. Drug Discov. Today 11:127‐132. | |
| A very current and very readable review of open‐source software and databases, with a special emphasis on their applications to drug discovery. | |
| Wishart, D.S. 2005. Bioinformatics in drug development and assessment. Drug Metab. Rev. 37:279‐310. | |
| This review touches on a number of the topics introduced in this section in somewhat more detail. The focus is more on predicting drug metabolism and drug toxicology. It is a good complement to the Jonsdottir et al. () paper. | |
| Internet Resources | |
| http://www.pharmabase.org | |
| Pharmabase is a cellular physiology and pharmacology database. | |
| http://www.ccdc.cam.ac.uk | |
| The Cambridge Structure Database contains the 3‐D coordinates of chemical structures that have been experimentally determined. | |
| http://cactus.nci.nih.gov/services/translate/ | |
| Cactus online Converter can take stick figure diagrams (MOL and SDF files) or SMILES strings and generate high quality 3‐D coordinates in PDB file format. | |
| http://cactus.nci.nih.gov/ncidb2/download.html | |
| Web site containing downloadable structure files of NCI Open database compounds. | |
| http://iris12.colby.edu/∼www/sconv.cgi | |
| Web site for Molecular Structure File Converter, which facilitates conversion between MOL, SDF, PDB, SMILES, and InChI formats. | |
| http://cactus.nci.nih.gov/services/translate/ | |
| Cactus Structure File Converter, which facilitates conversion between MOL, SDF, PDB, SMILES, and InChI formats. | |
| http://inchi.info/converter_en.html | |
| InChI converter, used to facilitate conversion between MOL, SDF, PDB, SMILES, and InChI formats. | |
| http://www.actelion.com/uninet/www/www_main_p.nsf/Content/Technologies+Property+Explorer | |
| Web site for the Actelion Property explorer a Web‐enabled Java applet that allows users to draw chemical structures and then rapidly calculate various drug‐related properties. | |
| http://preadmet.bmdrc.org/preadmet/index.php | |
| Web site for Pre‐ADMET, which offers a wide range of ADME and toxicological property calculations for any submitted chemical compound. |
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