Cheminformatics
From Free net encyclopedia
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. Also known as chemoinformatics and chemical informatics, these techniques are used in pharmaceutical companies in the process of Drug Discovery.
Contents |
History
The term (chemical) graph was introduced by Cullen in 1758 (Bonchev,1990). He used those graphs for affinity diagrams showing a relationship between chemical substances. Those results have never been published officially.
The term Chemoinformatics was defined by F.K. Brown in 1998:
- Chemoinformatics is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization. (Brown, 1998).
Since this, the term has evolved to be established as Cheminformatics [1].
Basics
Cheminformatics combines the scientific working fields of Chemistry and Computer science especially in the area of chemical Graph theory (Bonchev/Rouvray, 1990) and mining the chemical space. It is to be expected that the chemical space contains at least <math>10^{62}</math> molecules (Lahana, 1999).
Applications
Screening
Creation of large in silico virtual libraries of compounds using Combinatorial chemistry techniques to increase the efficiency in mining the chemical space. The post-QSAR technologies enable researchers to create the focused (targeted) hit compound libraries, that are the libraries of small molecules, which are ranked according to their accurately calculated constant affinity to a particular protein disease biological target and pre-defined toxicology profile. So now this virtual screening procedure considerably reduces time and costs in drug discovery.
Quantitative Structure Activity Relationship (QSAR)
Calculation of Quantitative Structure Activity Relationship and Quantitative Structure Property Relationship values, used to predict the activity of compounds from their structures. In this context there is also a strong relationship to Chemometrics.
File formats
In silico representation of chemical structures, using formats such as the XML based Chemical Markup Language, or SMILES. These representations are often used for storage in large chemical databases. See also Chemical file formats
Miscellaneous
- Statistics
- Data mining
- Unstructured data
- Structured data, e.g. string, tree, and graph mining
- Data analysis
- Scientific Visualization
Further reading
- F.K. Brown Chapter 35. Chemoinformatics: What is it and How does it Impact Drug Discovery. Annual Reports in Med. Chem., Ed. James A. Bristol, 1998, Vol. 33, pp. 375
- D. Bonchev, D.H. Rouvray: Chemical Graph Theory: Introduction and Fundamentals. Gordon and Breach Science Publishers, 1990, ISBN 0-85626-454-7.
- R. Lahana: How many leads from HTS?. Drug Discovery Today, 1999, 4, 447-448. DOI: 10.1016/S1359-6446(99)01393-8.
- Gasteiger J.(Editor), Engel T.(Editor): Chemoinformatics : A Textbook. John Wiley & Sons, 2004, ISBN 3-52730-681-1
- A.R. Leach, V.J. Gillet: An Introduction to Chemoinformatics. Springer, 2003, ISBN 1-4020-1347-7
- Brown, Frank. Editorial Opinion: Chemoinformatics – a ten year update Current Opinion in Drug Discovery & Development (2005), 8(3), 296-302.
See also
External links
- Comprehensive cheminformatics link list and data set repository: http://www.cheminformatics.org
- A cheminformatics glossary: http://www.genomicglossaries.com/content/chemoinformatics_gloss.asp
- XML- CML.ORG - The Site for Chemical Markup Language: http://www.xml-cml.org/
- VCCLAB Virtual Computational Chemistry Laboratory: http://www.vcclab.org
- Molecule mining: http://hms.liacs.nl/
- Famous Cheminformatics quotationsde:Cheminformatik