Cheminformatics
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The English used in this article may not be easy for everybody to understand. (December 2011) |
Cheminformatics (also known as chemoinformatics and chemical informatics) is the study of large amounts of chemical information. It is done mostly with the help of computers. These tools are used by pharmaceutical companies to discovery new drugs.
Cheminformatics uses computer science and information technology to help solve chemistry problems. Cheminformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software engineering, data mining, image processing, modeling and simulation, signal processing, discrete mathematics, control and system theory, circuit theory, and statistics, for generating new knowledge of chemistry.
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History [change]
The term chemoinformatics was defined by F.K. Brown [1][2] in 1998:
Basics [change]
Cheminformatics combines the scientific working fields of chemistry and computer science.[3][4] Cheminformatics can also be applied to data analysis for the paper, pulp and dye industries.
Uses [change]
Storage and retrieval [change]
The primary application of cheminformatics is in the storage of information relating to compounds. The efficient search of such stored information includes topics that are dealt with in computer science as data mining and machine learning.
File formats [change]
Computers represent chemical structures in specialized formats such as the XML-based Chemical Markup Language or SMILES. While some formats are suited for visual representations in 2 or 3 dimensions, others are more suited for studying physical interactions, modeling and docking studies.
Virtual libraries [change]
Chemical data can pertain to real or virtual molecules. Virtual compounds may be used to explore chemical space and predict new compounds with desired properties.
Virtual libraries of classes of compounds (drugs, natural products, diversity-oriented synthetic products) were recently generated using the FOG (fragment optimized growth) algorithm. [5]
Virtual screening [change]
Instead og testing the actual chemicals, virtual screening involves screening compounds by computer, to identify members likely to possess desired properties such as biological activity against a given target.
Quantitative structure-activity relationship (QSAR) [change]
This is to predict the activity of compounds from their structures. These studies link cheminofrmatics to chemometrics. Chemical expert systems are also relevant. They represent parts of chemical knowledge in computers.
References [change]
- ↑ F.K. Brown (1998). "Chapter 35. Chemoinformatics: What is it and How does it Impact Drug Discovery". Annual Reports in Med. Chem. 33: 375. doi:10.1016/S0065-7743(08)61100-8.
- ↑ Brown, Frank (2005). "Editorial Opinion: Chemoinformatics – a ten year update". Current Opinion in Drug Discovery & Development 8 (3): 296–302.
- ↑ Gasteiger J.(Editor), Engel T.(Editor): Chemoinformatics : A Textbook. John Wiley & Sons, 2004, ISBN 3-527-30681-1
- ↑ A.R. Leach, V.J. Gillet: An Introduction to Chemoinformatics. Springer, 2003, ISBN 1-4020-1347-7
- ↑ Kutchukian, Peter; Lou, David; Shakhnovich, Eugene (2009). "FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules occupying Druglike Chemical". Journal of Chemical Information and Modeling 49 (7): 1630–1642. doi:10.1021/ci9000458. PMID 19527020.
Other websites [change]
- OEChem Cheminformatics Programming Toolkit
- The Blue Obelisk Movement
- The eCheminfo Network and Community of Practice
- Cheminformatics at Indiana University
- Indiana Cheminformatics Education Portal
- Cheminformatics at Rensselaer Polytechnic Institute
- The Chemical Structure Association Trust (see also CSA Trust).
- Comprehensive cheminformatics link list and data set repository
- A cheminformatics glossary
- Chemoinformatics initiatives at NCL Pune, India
- International Conference on Chemoinformatics at NCL,Pune
- Chemical Informatics Education and Research at Indiana University
- Famous Cheminformatics quotations
- The Cheminformatics and QSAR Society
- UK-QSAR and ChemoInformatics Group
- Education and Research at the University of Hamburg
- Cheminformatics research at the Unilever Centre for Molecular Informatics, Cambridge, UK
- YACHS Yet Another CHemistry Summarizer, Laboratoire Informatique d'Avignon LIA, France
- Cheminformatics research at NovaMechanics Cyprus
- Weblink-Cheminformatics SW and DB
- Cheminformatics studies from Unilever Centre for Molecular Informatics to OpenEye
