Cheminformatics

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.

History

The term chemoinformatics was defined by F.K. Brown ^[1]^[2] in 1998:

Basics

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

Storage and retrieval

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

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

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

Instead of 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)

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

↑ 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. PMID 15892243.
↑ 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, P. S.; Lou, D.; Shakhnovich, E. I. (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

OEChem Cheminformatics Programming Toolkit
The Blue Obelisk Movement
The eCheminfo Archived 2020-01-03 at the Wayback Machine Network and Community of Practice
Cheminformatics at Indiana University Archived 2012-02-07 at the Wayback Machine
Indiana Cheminformatics Education Portal Archived 2010-10-14 at the Wayback Machine
Cheminformatics at Rensselaer Polytechnic Institute Archived 2022-04-08 at the Wayback Machine
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 Archived 2009-08-24 at the Wayback Machine
International Conference on Chemoinformatics at NCL,Pune Archived 2013-01-08 at Archive.today
Chemical Informatics Education Archived 2007-11-15 at the Wayback Machine and Research Archived 2010-10-22 at the Wayback Machine at Indiana University
Famous Cheminformatics quotations Archived 2006-06-14 at the Wayback Machine
The Cheminformatics and QSAR Society
UK-QSAR and ChemoInformatics Group
Education and Research at the University of Hamburg Archived 2009-04-30 at the Wayback Machine
Cheminformatics research at the Unilever Centre for Molecular Informatics, Cambridge, UK Archived 2010-02-21 at the Wayback Machine
YACHS Yet Another CHemistry Summarizer, Laboratoire Informatique d'Avignon LIA, France Archived 2011-03-16 at the Wayback Machine
Cheminformatics research at NovaMechanics Cyprus
Weblink-Cheminformatics SW and DB Archived 2023-08-28 at the Wayback Machine
Cheminformatics studies from Unilever Centre for Molecular Informatics to OpenEye

[Brown_1998-1] 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.

[2] Brown, Frank (2005). "Editorial Opinion: Chemoinformatics – a ten year update". Current Opinion in Drug Discovery & Development. 8 (3): 296–302. PMID 15892243.

[Gasteiger_2004-3] Gasteiger J.(Editor), Engel T.(Editor): Chemoinformatics : A Textbook. John Wiley & Sons, 2004, ISBN 3-527-30681-1

[4] A.R. Leach, V.J. Gillet: An Introduction to Chemoinformatics. Springer, 2003, ISBN 1-4020-1347-7

[5] Kutchukian, P. S.; Lou, D.; Shakhnovich, E. I. (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.

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