Editing Cheminformatics

{{Short description|Computational chemistry}}
{{more citations needed|date=February 2020}}
'''Cheminformatics''' (also known as '''chemoinformatics''') refers to the use of [[physical chemistry]] theory with [[computer science|computer]] and [[information science]] techniques—so called "''[[in silico]]''" techniques—in application to a range of descriptive and prescriptive problems in the field of [[chemistry]], including in its applications to [[biochemistry|biology]] and [[molecular biology|related molecular fields]]. Such ''[[in silico]]'' techniques are used, for example, by [[pharmaceutical companies]] and in academic settings to aid and inform the process of [[drug discovery]], for instance in the design of well-defined [[combinatorial libraries]] of synthetic compounds, or to assist in [[structure-based drug design]]. The methods can also be used in chemical and allied industries, and such fields as [[environmental science]] and [[pharmacology]], where chemical processes are involved or studied.<ref>{{cite journal|title=Basic Overview of Chemoinformatics|author=Thomas Engel|journal=J. Chem. Inf. Model.|year=2006|volume=46|issue=6|pages=2267–77|doi=10.1021/ci600234z|pmid=17125169}}</ref>

== History ==
Cheminformatics has been an active field in various guises since the 1970s and earlier, with activity in academic departments and commercial pharmaceutical research and development departments.<ref>{{cite book|author = Martin, Yvonne Connolly | author-link = Yvonne Connolly Martin | date=1978| title=Quantitative Drug Design: A Critical Introduction|series = Medicinal Research series | volume = 8 | location=New York, NY | publisher= [[Marcel Dekker]] |isbn = 9780824765743 | edition = 1st }}</ref>{{page needed|date=February 2020}}{{citation needed|date=February 2020}} The term chemoinformatics was defined in its application to drug discovery by F.K. Brown in 1998:<ref name="Brown_1998">{{Cite book | author = F.K. Brown | chapter = Ch. 35. Chemoinformatics: What is it and How does it Impact Drug Discovery | title = Annual Reports in Medicinal Chemistry | year = 1998 | volume = 33 | pages = 375–384 | doi = 10.1016/S0065-7743(08)61100-8 | isbn = 9780120405336}};{{page needed|date=February 2020}} see also {{cite journal | author = Brown, Frank | title = Chemoinformatics–A Ten Year Update | format =  | journal = [[Current Opinion in Drug Discovery & Development]]| year = 2005 | volume = 8 | issue = 3 | pages = 296–302}}</ref><blockquote>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.</blockquote> Since then, both terms, cheminformatics and chemoinformatics, have been used,{{citation needed|date=February 2020}} although, [[lexicography|lexicographically]], cheminformatics appears to be more frequently used,{{when|date=February 2020}}<ref>{{Cite web|url=http://www.molinspiration.com/chemoinformatics.html|title=Cheminformatics or Chemoinformatics ?|access-date=2006-03-31|archive-date=2017-06-21|archive-url=https://web.archive.org/web/20170621112022/http://www.molinspiration.com/chemoinformatics.html|url-status=dead}}</ref><ref>{{Cite web|url=http://www.genomicglossaries.com/content/glossary_faq.asp#3|title = Biopharmaceutical glossary Tips & FAQs}}</ref> despite academics in Europe declaring for the variant chemoinformatics in 2006.<ref>{{Cite web |title=The Obernai Declaration |url=https://infochim.u-strasbg.fr/chemoinformatics/Obernai%20Declaration.pdf |url-status=live |archive-url=https://web.archive.org/web/20160303192029/http://infochim.u-strasbg.fr/chemoinformatics/Obernai%20Declaration.pdf |archive-date=March 3, 2016 |website=Chéminformatique Strasbourg}}</ref> In 2009, a prominent Springer journal in the field was founded by transatlantic executive editors named the [[Journal of Cheminformatics]].<ref>{{Cite web |last=Willighagen |first=Egon |title=Open Access Journal of Cheminformatics now live! « SteinBlog |url=http://www.steinbeck-molecular.de/steinblog/index.php/2009/03/17/open-access-journal-of-cheminformatics-now-live/ |access-date=2022-06-20 |language=en-US}}</ref>

== Background ==
Cheminformatics combines the scientific working fields of chemistry, computer science, and information science—for example in the areas of [[topology (chemistry)|topology]], [[chemical graph theory]], [[information retrieval]] and [[data mining]] in the [[chemical space]].<ref name="Gasteiger_2004">{{cite book|editor= Gasteiger J. |editor2=Engel T. | date=2004 | title=Chemoinformatics: A Textbook |location=New York, NY | publisher=Wiley|isbn = 3527306811 }}</ref>{{page needed|date=February 2020}}<ref>{{cite book|author1 = Leach, A.R. |author2 =Gillet, V.J. | date=2003 | title=An Introduction to Chemoinformatics |location=Berlin, DE | publisher=Springer|isbn = 1402013477 }}</ref>{{page needed|date=February 2020}}<ref name="Varnek_2011a">{{cite journal | author1 = Varnek, A. | author2 = Baskin, I. | year = 2011 | title = Chemoinformatics as a Theoretical Chemistry Discipline | journal = Molecular Informatics | volume = 30 | issue = 1 | pages = 20–32 | doi=10.1002/minf.201000100| pmid = 27467875 | s2cid = 21604072 }}</ref><ref name="Bunin_2006">{{cite book|author1= Bunin, B.A. |author2=Siesel, B. |author3=Morales, G. |author4=Bajorath J. | date=2006 | title=Chemoinformatics: Theory, Practice, & Products |location=New York, NY | publisher=Springer|isbn = 9781402050008 }}</ref>{{page needed|date=February 2020}} Cheminformatics can also be applied to data analysis for various industries like [[paper industry|paper]] and [[pulp industry|pulp]], dyes and such allied industries.<ref>{{Cite web |last1=Williams |first1=Tova |last2=University |first2=North Carolina State |title=Cheminformatics approaches to creating new hair dyes |url=https://phys.org/news/2018-10-cheminformatics-approaches-hair-dyes.html |access-date=2022-06-20 |website=phys.org |language=en}}</ref>

== Applications ==
===Storage and retrieval===
{{unreferenced section|date=February 2020}}
{{main|Chemical database}}
A primary application of cheminformatics is the storage, indexing, and search of information relating to chemical compounds.{{cn|date=March 2025}} The efficient search of such stored information includes topics that are dealt with in computer science, such as data mining, information retrieval, [[information extraction]], and [[machine learning]].{{citation needed|date=February 2020}} Related research topics include:{{citation needed|date=February 2020}}
{{div col}}
* [[Digital libraries]]
* [[Unstructured data]]
* [[Structured data mining]] and mining of [[structured data]]
**[[Database mining]]
**[[Graph mining]]
**[[Molecule mining]]
**[[Sequence mining]]
**[[Tree mining]]
{{div col end}}

==== File formats ====
{{main|Chemical file format}}
The ''in silico'' representation of chemical structures uses specialized formats such as the [[Simplified molecular input line entry specification]]s (SMILES)<ref>{{cite journal|title=SMILES, a Chemical Language and Information System: 1: Introduction to Methodology and Encoding Rules|author=Weininger, David|journal=Journal of Chemical Information and Modeling|year=1988|volume=28|issue=1|pages=31–36|doi=10.1021/ci00057a005|s2cid=5445756 }}</ref> or the [[XML]]-based [[Chemical Markup Language]].<ref>{{cite journal|title=Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles|author=Murray-Rust, Peter|author2=Rzepa, Henry S.|journal=Journal of Chemical Information and Computer Sciences|year=1999|volume=39|issue=6|pages=928–942|doi=10.1021/ci990052b}}</ref>  These representations are often used for storage in large [[chemical database]]s.{{citation needed|date=February 2020}} While some formats are suited for visual representations in two- or three-dimensions, others are more suited for studying physical interactions, modeling and docking studies.{{citation needed|date=February 2020}}

=== Virtual libraries ===
{{primary sources|section|date=February 2020}}
Chemical data can pertain to real or virtual molecules.  Virtual libraries of compounds may be generated in various ways to explore chemical space and hypothesize novel 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.<ref>{{cite journal|title=FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules occupying Druglike Chemical | last=Kutchukian | first=Peter  |author2=Lou, David |author3=Shakhnovich, Eugene  |journal=Journal of Chemical Information and Modeling | year=2009 |volume=49 | pages=1630–1642|doi=10.1021/ci9000458|pmid=19527020|issue=7 }}</ref>  This was done by using cheminformatic tools to train transition probabilities of a [[Markov chain]] on authentic classes of compounds, and then using the Markov chain to generate novel compounds that were similar to the training database.

=== Virtual screening ===
{{unreferenced section|date=February 2020}}
{{main|Virtual screening}}
In contrast to [[high-throughput screening]], virtual screening involves computationally
screening ''in silico'' libraries of compounds, by means of various methods such as
[[docking (molecular)|docking]], to identify members likely to possess desired properties
such as [[biological activity]] against a given target. In some cases, [[combinatorial chemistry]] is used in the development of the library to increase the efficiency in mining the chemical space. More commonly, a diverse library of small molecules or [[natural product]]s is screened.

===Quantitative structure-activity relationship (QSAR)===
{{main|Quantitative structure–activity relationship}}
This is the 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]]. Chemical [[expert system]]s are also relevant, since they represent parts of chemical knowledge as an ''in silico'' representation. There is a relatively new concept of [[matched molecular pair analysis]] or prediction-driven MMPA which is coupled with QSAR model in order to identify activity cliff.<ref name="Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process">{{Cite journal | doi=10.1186/s13321-014-0048-0| pmid=25544551| pmc=4272757| title=Prediction-driven matched molecular pairs to interpret QSARs and aid the molecular optimization process| journal=Journal of Cheminformatics| volume=6| issue=1| pages=48| year=2014| last1=Sushko| first1=Yurii| last2=Novotarskyi| first2=Sergii| last3=Körner| first3=Robert| last4=Vogt| first4=Joachim| last5=Abdelaziz| first5=Ahmed| last6=Tetko| first6=Igor V.| doi-access=free}}</ref>

== See also ==
{{div col}}
* [[Bioinformatics]]
* [[Chemical file format]]
* [[Chemicalize.org]]
* [[Cheminformatics toolkits]]
* [[Chemogenomics]]
* [[Computational chemistry]]
* [[Information engineering]]
* [[Journal of Chemical Information and Modeling]]
* [[Journal of Cheminformatics]]
* [[Materials informatics]]
* [[Molecular design software]]
* [[Molecular graphics]]
* [[Molecular Informatics]]
* [[Molecular modelling]]
* [[Nanoinformatics]]
* [[List of software for molecular mechanics modeling|Software for molecular modeling]]
* [[WorldWide Molecular Matrix]]
* [[Molecular descriptor]]
{{div col end}}

==References==
<references/>

==Further reading==
* {{cite journal|author=Engel, Thomas|year=2006|title=Basic Overview of Chemoinformatics|journal=J. Chem. Inf. Model.|volume=46|issue=6|pages=2267–2277|doi=10.1021/ci600234z|pmid=17125169}}
* {{cite book|author = Martin, Yvonne Connolly | author-link = Yvonne Connolly Martin | date=2010| title=Quantitative Drug Design: A Critical Introduction|location=Boca Raton, FL | publisher=CRC Press–Taylor & Francis|isbn = 9781420070996 | edition = 2nd }}
* {{cite book|author1 = Leach, A.R. |author2=Gillet, V.J. | date=2003 | title=An Introduction to Chemoinformatics |location=Berlin, DE | publisher=Springer|isbn = 1402013477 }}
* {{cite book|editor= Gasteiger J. |editor2=Engel T. | date=2004 | title=Chemoinformatics: A Textbook |location=New York, NY | publisher=Wiley|isbn = 3527306811 }}
* {{cite journal | author = Varnek, A. |author2=Baskin, I. | year = 2011 | title = Chemoinformatics as a Theoretical Chemistry Discipline | journal = Molecular Informatics | volume = 30 | issue = 1 | pages = 20–32 | doi=10.1002/minf.201000100| pmid = 27467875 |s2cid=21604072 }}
* {{cite book|author1 = Bunin, B.A. |author2=Siesel, B. |author3=Morales, G. |author4=Bajorath J. | date=2006 | title=Chemoinformatics: Theory, Practice, & Products |location=New York, NY | publisher=Springer|isbn = 9781402050008 }}

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