Chemical informatics - Revision history

Shawndouglas: Cats

2022-09-17T16:46:15Z

Cats

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	{{Reflist\|colwidth=30em}}		{{Reflist\|colwidth=30em}}

			<!---Place all category tags here-->
			[[Category:Chemical industry]]
	[[Category:Informatics]]		[[Category:Informatics]]

Shawndouglas: Updated URLs for 2022

2022-01-06T19:57:50Z

Updated URLs for 2022

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	* [https://csa-trust.org/ The Chemical Structure Association Trust]		* [https://csa-trust.org/ The Chemical Structure Association Trust]
	* [http://www.echeminfo.com/ The eCheminfo Network and Community of Practice]		* [http://www.echeminfo.com/ The eCheminfo Network and Community of Practice]
	* [~~http~~://~~www.~~ukqsar.org The UK-QSAR and ChemoInformatics Group]		* [https://ukqsar.org/ The UK-QSAR and ChemoInformatics Group]

	==Notes==		==Notes==

	This article reuses portions of content from [~~http~~://en.wikipedia.org/wiki/Cheminformatics the Wikipedia article].		This article reuses portions of content from [https://en.wikipedia.org/wiki/Cheminformatics the Wikipedia article].

	==References==		==References==

Shawndouglas: Minor updates for 2020

2020-03-20T18:31:24Z

Minor updates for 2020

← Older revision		Revision as of 18:31, 20 March 2020
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	[[File:Jmol1.png\|\|thumb\|400px\|right\|The Jmol open-source Java viewer for chemical 3D structures is an example of a software application that may be used in the field of chemical informatics.]]		[[File:Jmol1.png\|\|thumb\|400px\|right\|The Jmol open-source Java viewer for chemical 3D structures is an example of a software application that may be used in the field of chemical informatics.]]
	'''Chemical informatics''' (more commonly known as '''chemoinformatics''' and '''cheminformatics''') is the use of computer and informational techniques applied to a range of problems in the field of chemistry. While the field has roughly been around around since the 1990s, the rise in high-throughput screening (a scientific experimentation method primarily used in drug discovery) and combinatorial chemistry (a method of synthesizing a large number of compounds in a single process), as well as increases in computing power and data storage sizes, have increased interest in the field in the twenty-first century.<ref name="LeachIntroChem">{{cite book \|url=~~http~~://books.google.com/books?id=4z7Q87HgBdwC&printsec=frontcover \|title=An Introduction to Chemoinformatics \|author=Leach, ~~Andrew~~ R.; Gillet, ~~Valerie~~ J. \|publisher=Springer \|version=Revised \|year=2007 \|pages=256 \|isbn=9781402062902 \|accessdate=~~19 May 2014~~}}</ref>		'''Chemical informatics''' (more commonly known as '''chemoinformatics''' and '''cheminformatics''') is the use of computer and informational techniques applied to a range of problems in the field of chemistry. While the field has roughly been around around since the 1990s, the rise in high-throughput screening (a scientific experimentation method primarily used in drug discovery) and combinatorial chemistry (a method of synthesizing a large number of compounds in a single process), as well as increases in computing power and data storage sizes, have increased interest in the field in the twenty-first century.<ref name="LeachIntroChem">{{cite book \|url=https://books.google.com/books?id=4z7Q87HgBdwC&printsec=frontcover \|title=An Introduction to Chemoinformatics \|author=Leach, A.R.; Gillet, V.J. \|publisher=Springer \|version=Revised \|year=2007 \|pages=256 \|isbn=9781402062902 \|accessdate=20 March 2020}}</ref>

	Outside of pharmaceutical research, other applications of chemical informatics include the area of topology, chemical graph theory, and mining the chemical space. It can also be applied to data analysis for the paper, pulp, and dye industries.<ref name="Gasteiger2006">{{cite book \|url=~~http~~://books.google.com/books?id=LCD-1vHBHIAC&printsec=frontcover \|title=Chemoinformatics: A Textbook \|chapter=Chapter 1: Introduction \|author=Gasteiger, ~~Johann~~ (ed.) ; Engel, ~~Thomas~~ (ed.) \|publisher=John Wiley & Sons \|year=2006 \|pages=1–14 \|isbn=9783527606504}}</ref><ref name="LeachIntroChem" />		Outside of pharmaceutical research, other applications of chemical informatics include the area of topology, chemical graph theory, and mining the chemical space. It can also be applied to data analysis for the paper, pulp, and dye industries.<ref name="Gasteiger2006">{{cite book \|url=https://books.google.com/books?id=LCD-1vHBHIAC&printsec=frontcover \|title=Chemoinformatics: A Textbook \|chapter=Chapter 1: Introduction \|author=Gasteiger, J. (ed.) ; Engel, T. (ed.) \|publisher=John Wiley & Sons \|year=2006 \|pages=1–14 \|isbn=9783527606504 \|accessdate=20 March 2020}}</ref><ref name="LeachIntroChem" />

	==History==		==History==
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	The 1960s saw the introduction of databases for the storage and retrieval of chemical structures, as well as three-dimensional molecular modeling methods, laying the groundwork for future generations to improve computational methods of chemical and molecular analysis.<ref name="Gasteiger2006" />		The 1960s saw the introduction of databases for the storage and retrieval of chemical structures, as well as three-dimensional molecular modeling methods, laying the groundwork for future generations to improve computational methods of chemical and molecular analysis.<ref name="Gasteiger2006" />

	The term "chemoinformatics" was defined by F.K. Brown<ref name="Brown1998">{{cite journal ~~\|url=http://www.sciencedirect.com/science/article/pii/S0065774308611008 \|journal=Annual Reports in Medicinal Chemistry~~ \|title=Chapter 35. Chemoinformatics: What is it and how does it impact drug discovery \|author=Brown, F.K. ~~\|year=1998~~ \|volume=33 \|pages=375–384 \|doi=10.1016/S0065-7743(08)61100-8}}</ref><ref>{{cite journal \|~~url~~=~~http~~:~~//www.ncbi.nlm.nih.gov/pubmed/15892243~~ \|journal=Current Opinion in Drug Discovery & Development ~~\|title=Editorial Opinion: Chemoinformatics – a ten year update~~ \|author=Brown, ~~Frank~~ \|year=May 2005 \|volume=8 \|issue=3 \|pages=298–302}}</ref> in 1998 as such:		The term "chemoinformatics" was defined by F.K. Brown<ref name="Brown1998">{{cite journal \|title=Chapter 35. Chemoinformatics: What is it and how does it impact drug discovery \|journal=Annual Reports in Medicinal Chemistry \|author=Brown, F.K. \|volume=33 \|pages=375–384 \|year=1998 \|doi=10.1016/S0065-7743(08)61100-8}}</ref><ref>{{cite journal \|title=Editorial Opinion: Chemoinformatics – A ten year update \|journal=Current Opinion in Drug Discovery & Development \|author=Brown, F. \|year=May 2005 \|volume=8 \|issue=3 \|pages=298–302 \|pmid=15892243}}</ref> in 1998 as such:

	<blockquote>		<blockquote>
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	Since then, both the "chem" and "chemo" spellings have been used. European academia settled on the term "chemoinformatics" for its ~~2006 Obernai~~ research and teaching ~~workshop~~.<ref name="Obernai">{{cite web \|url=http://infochim.u-strasbg.fr/~~chemoinformatics/~~ \|title=~~Workshop Chemoinformatics in Europe: Research and Teaching~~ \|publisher=Laboratoire de Chémoinformatique, University of Strasbourg ~~\|year=2006~~ \|accessdate=~~19 May 2014~~}}</ref> Other entities like the Journal of Cheminformatics and Slovak company Molinspiration have trended towards "cheminformatics."<ref name="MolChem">{{cite web \|url=~~http~~://www.molinspiration.com/chemoinformatics.html \|title=Cheminformatics or Chemoinformatics? \|publisher=Molinspiration Cheminformatics \|date=December 2009 \|accessdate=~~19 May 2014~~}}</ref><ref name="JournChem">{{cite web \|url=~~http~~://~~www~~.~~jcheminf~~.com/~~about~~ \|title=About ''Journal of Cheminformatics'' \|publisher=~~Chemistry~~ Central \|accessdate=~~19 May 2014~~}}</ref>		Since then, both the "chem" and "chemo" spellings have been used. European academia has seemingly settled on the term "chemoinformatics" for many of its research and teaching workshops.<ref name="Obernai">{{cite web \|url=http://infochim.u-strasbg.fr/spip.php?rubrique11 \|title=Conferences - Chémoinformatique Strasbourg \|publisher=Laboratoire de Chémoinformatique, University of Strasbourg \|accessdate=20 March 2020}}</ref> Other entities like the ''Journal of Cheminformatics'' and Slovak company Molinspiration have trended towards "cheminformatics."<ref name="MolChem">{{cite web \|url=https://www.molinspiration.com/chemoinformatics.html \|title=Cheminformatics or Chemoinformatics? \|publisher=Molinspiration Cheminformatics \|date=December 2009 \|accessdate=20 March 2020}}</ref><ref name="JournChem">{{cite web \|url=https://jcheminf.biomedcentral.com/ \|title=About ''Journal of Cheminformatics'' \|publisher=BioMed Central Ltd \|accessdate=20 March 2020}}</ref>

	==Application==		==Application==

	===Storage and retrieval===		===Storage and retrieval===
	The primary application of chemical informatics is in the storage and retrieval of both structured and unstructured information relating to chemical structures, molecular models and other chemical data. Efficiently querying and retrieving that stored information extends into other realms of computer science like data mining and machine learning. Other forms of data querying include graph, molecule, sequence, and tree mining.<ref name="Gasteiger2006Ch2">{{cite book \|url=~~http~~://books.google.com/books?id=LCD-1vHBHIAC&printsec=frontcover \|title=Chemoinformatics: A Textbook \|chapter=Chapter 2: Representation of Chemical Compounds \|author=Gasteiger, ~~Johann~~ (ed.) ; Engel, ~~Thomas~~ (ed.) \|publisher=John Wiley & Sons \|year=2006 \|pages=15–157 \|isbn=9783527606504}}</ref>		The primary application of chemical informatics is in the storage and retrieval of both structured and unstructured information relating to chemical structures, molecular models and other chemical data. Efficiently querying and retrieving that stored information extends into other realms of computer science like data mining and machine learning. Other forms of data querying include graph, molecule, sequence, and tree mining.<ref name="Gasteiger2006Ch2">{{cite book \|url=https://books.google.com/books?id=LCD-1vHBHIAC&printsec=frontcover \|title=Chemoinformatics: A Textbook \|chapter=Chapter 2: Representation of Chemical Compounds \|author=Gasteiger, J. (ed.) ; Engel, T. (ed.) \|publisher=John Wiley & Sons \|year=2006 \|pages=15–157 \|isbn=9783527606504 \|accessdate=20 March 2020}}</ref>

	===Representation===		===Representation===
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	===Virtual libraries===		===Virtual libraries===
	Stored chemical data can pertain to both real and virtual molecules. Virtual libraries of such molecules and compounds may be generated in various ways to explore chemical space and hypothesize novel compounds with desired properties. The Fragment Optimized Growth (FOG) algorithm, for example, was developed to "grow" novel classes of compounds like drugs, natural products, and diversity-oriented synthetic products from a training database of existing compounds.<ref name="KutchFOG">{{cite journal ~~\|url=http://pubs.acs.org/doi/abs/10.1021/ci9000458 \|journal=Journal of Chemical Information and Modeling~~ \|title=FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space \|author=Kutchukian, ~~Peter~~ S.; Lou, ~~David~~; Shakhnovich, ~~Eugene~~ I. ~~\|year=2009~~ \|volume=49 \|issue=7 \| pages=1630–1642 \|doi=10.1021/ci9000458 \|pmid=19527020}}</ref><ref name="SchneiderDeNovo">{{cite book \|url=~~http~~://books.google.com/books?id=~~Jf1QAQAAQBAJ~~&pg=PA311 \|chapter=Chapter 13: Construction of Drug-Like Compounds by Markov Chains \|title=De novo Molecular Design \|author=Kutchukian, ~~Peter~~ S.; Virtanen, ~~Salla~~ I.; Lounkine, ~~Eugen; Glick, Meir; Shakhnovich, Eugene I~~.~~; Schneider, Gisbert (ed~~.) \|publisher=John Wiley & Sons \|year=2013 \|isbn=9783527677009 \|accessdate=~~19 May 2014~~}}</ref>		Stored chemical data can pertain to both real and virtual molecules. Virtual libraries of such molecules and compounds may be generated in various ways to explore chemical space and hypothesize novel compounds with desired properties. The Fragment Optimized Growth (FOG) algorithm, for example, was developed to "grow" novel classes of compounds like drugs, natural products, and diversity-oriented synthetic products from a training database of existing compounds.<ref name="KutchFOG">{{cite journal \|title=FOG: Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space \|journal=Journal of Chemical Information and Modeling \|author=Kutchukian, P.S.; Lou, D.; Shakhnovich, E.I. \|volume=49 \|issue=7 \| pages=1630–1642 \|year=2009 \|doi=10.1021/ci9000458 \|pmid=19527020}}</ref><ref name="SchneiderDeNovo">{{cite book \|url=https://books.google.com/books?id=1QFRAQAAQBAJ&pg=PA311 \|chapter=Chapter 13: Construction of Drug-Like Compounds by Markov Chains \|title=De novo Molecular Design \|author=Kutchukian, P.S.; Virtanen, S.I.; Lounkine, E. et al. \|publisher=John Wiley & Sons \|year=2013 \|isbn=9783527677009 \|accessdate=20 March 2020}}</ref>

	===Virtual screening===		===Virtual screening===
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	== External links ==		== External links ==
	* [http://www.genomicglossaries.com/content/chemoinformatics_gloss.asp Cambridge Healthtech Institute Cheminformatics/ Chemoinformatics Glossary & Taxonomy]		* [http://www.genomicglossaries.com/content/chemoinformatics_gloss.asp Cambridge Healthtech Institute Cheminformatics/ Chemoinformatics Glossary & Taxonomy]
	* [http://icep.wikispaces.com/ Indiana Cheminformatics Education Portal]		* [https://web.archive.org/web/20170928055641/http://icep.wikispaces.com/ Indiana Cheminformatics Education Portal] (Archived)
	* [~~http~~://~~www~~.~~blueobelisk~~.~~org~~/ The Blue Obelisk Project]		* [https://blueobelisk.github.io/ The Blue Obelisk Project]
	* [~~http~~://~~www.~~csa-trust.org The Chemical Structure Association Trust]		* [https://csa-trust.org/ The Chemical Structure Association Trust]
	* [http://www.echeminfo.com/ The eCheminfo Network and Community of Practice]		* [http://www.echeminfo.com/ The eCheminfo Network and Community of Practice]
	* [http://www.ukqsar.org The UK-QSAR and ChemoInformatics Group]		* [http://www.ukqsar.org The UK-QSAR and ChemoInformatics Group]
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	==References==		==References==
	~~<references/>~~		{{Reflist\|colwidth=30em}}

	[[Category:Informatics]]		[[Category:Informatics]]

Shawndouglas: /* Representation */ Internal link

2014-08-22T16:40:10Z

Representation: Internal link

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	===Representation===		===Representation===
	The ''in silico'' representation of chemical structures uses specialized formats such as the XML-based Chemical Markup Language or Simplified Molecular-Input Line-Entry System (SMILES) specifications. These representations are often used for storage in large chemical databases. 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.<ref name="Gasteiger2006Ch2" />		The ''in silico'' representation of chemical structures uses specialized formats such as the [[XML]]-based Chemical Markup Language or Simplified Molecular-Input Line-Entry System (SMILES) specifications. These representations are often used for storage in large chemical databases. 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.<ref name="Gasteiger2006Ch2" />

	===Virtual libraries===		===Virtual libraries===

Shawndouglas: Grammar

2014-05-19T22:00:42Z

Grammar

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	[[File:Jmol1.png\|\|thumb\|400px\|right\|The Jmol open-source Java viewer for chemical 3D structures is an example of an application that may be used in the field of chemical informatics.]]		[[File:Jmol1.png\|\|thumb\|400px\|right\|The Jmol open-source Java viewer for chemical 3D structures is an example of a software application that may be used in the field of chemical informatics.]]
	'''Chemical informatics''' (more commonly known as '''chemoinformatics''' and '''cheminformatics''') is the use of computer and informational techniques applied to a range of problems in the field of chemistry. While the field has roughly been around around since the 1990s, the rise in high-throughput screening (a scientific experimentation method primarily used in drug discovery) and combinatorial chemistry (a method of synthesizing a large number of compounds in a single process), as well as increases in computing power and data storage sizes, have increased interest in the field in the twenty-first century.<ref name="LeachIntroChem">{{cite book \|url=http://books.google.com/books?id=4z7Q87HgBdwC&printsec=frontcover \|title=An Introduction to Chemoinformatics \|author=Leach, Andrew R.; Gillet, Valerie J. \|publisher=Springer \|version=Revised \|year=2007 \|pages=256 \|isbn=9781402062902 \|accessdate=19 May 2014}}</ref>		'''Chemical informatics''' (more commonly known as '''chemoinformatics''' and '''cheminformatics''') is the use of computer and informational techniques applied to a range of problems in the field of chemistry. While the field has roughly been around around since the 1990s, the rise in high-throughput screening (a scientific experimentation method primarily used in drug discovery) and combinatorial chemistry (a method of synthesizing a large number of compounds in a single process), as well as increases in computing power and data storage sizes, have increased interest in the field in the twenty-first century.<ref name="LeachIntroChem">{{cite book \|url=http://books.google.com/books?id=4z7Q87HgBdwC&printsec=frontcover \|title=An Introduction to Chemoinformatics \|author=Leach, Andrew R.; Gillet, Valerie J. \|publisher=Springer \|version=Revised \|year=2007 \|pages=256 \|isbn=9781402062902 \|accessdate=19 May 2014}}</ref>

Shawndouglas: Added image.

2014-05-19T22:00:15Z

Added image.

← Older revision		Revision as of 22:00, 19 May 2014
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			[[File:Jmol1.png\|\|thumb\|400px\|right\|The Jmol open-source Java viewer for chemical 3D structures is an example of an application that may be used in the field of chemical informatics.]]
	'''Chemical informatics''' (more commonly known as '''chemoinformatics''' and '''cheminformatics''') is the use of computer and informational techniques applied to a range of problems in the field of chemistry. While the field has roughly been around around since the 1990s, the rise in high-throughput screening (a scientific experimentation method primarily used in drug discovery) and combinatorial chemistry (a method of synthesizing a large number of compounds in a single process), as well as increases in computing power and data storage sizes, have increased interest in the field in the twenty-first century.<ref name="LeachIntroChem">{{cite book \|url=http://books.google.com/books?id=4z7Q87HgBdwC&printsec=frontcover \|title=An Introduction to Chemoinformatics \|author=Leach, Andrew R.; Gillet, Valerie J. \|publisher=Springer \|version=Revised \|year=2007 \|pages=256 \|isbn=9781402062902 \|accessdate=19 May 2014}}</ref>		'''Chemical informatics''' (more commonly known as '''chemoinformatics''' and '''cheminformatics''') is the use of computer and informational techniques applied to a range of problems in the field of chemistry. While the field has roughly been around around since the 1990s, the rise in high-throughput screening (a scientific experimentation method primarily used in drug discovery) and combinatorial chemistry (a method of synthesizing a large number of compounds in a single process), as well as increases in computing power and data storage sizes, have increased interest in the field in the twenty-first century.<ref name="LeachIntroChem">{{cite book \|url=http://books.google.com/books?id=4z7Q87HgBdwC&printsec=frontcover \|title=An Introduction to Chemoinformatics \|author=Leach, Andrew R.; Gillet, Valerie J. \|publisher=Springer \|version=Revised \|year=2007 \|pages=256 \|isbn=9781402062902 \|accessdate=19 May 2014}}</ref>

Shawndouglas: Updated content and added citations.

2014-05-19T21:55:26Z

Updated content and added citations.

Show changes

Shawndouglas at 22:12, 24 April 2014

2014-04-24T22:12:16Z

← Older revision		Revision as of 22:12, 24 April 2014
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	~~''(This article was taken from Wikipedia)''~~

	'''Cheminformatics''' (also known as '''chemoinformatics''' and '''chemical informatics''') is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These ''in silico'' techniques are used in pharmaceutical companies in the process of [[drug design\|drug discovery]]. These methods can also be used in chemical and allied industries in various other forms.		'''Cheminformatics''' (also known as '''chemoinformatics''' and '''chemical informatics''') is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These ''in silico'' techniques are used in pharmaceutical companies in the process of [[drug design\|drug discovery]]. These methods can also be used in chemical and allied industries in various other forms.

Shawndouglas: Added attribution.

2014-04-24T22:12:01Z

Added attribution.

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	* [[Bioinformatics]]		* [[Bioinformatics]]
	* [[Data analysis]]		* [[Data analysis]]

	~~==References==~~
	~~<references/>~~

	== External links ==		== External links ==
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	* [http://www.qspr.pe.kr/my/index.php?option=com_bookmarks&Itemid=28 Weblink-Cheminformatics SW and DB]		* [http://www.qspr.pe.kr/my/index.php?option=com_bookmarks&Itemid=28 Weblink-Cheminformatics SW and DB]
	* [http://chemoinformatician.co.uk Cheminformatics studies from Unilever Centre for Molecular Informatics to OpenEye]		* [http://chemoinformatician.co.uk Cheminformatics studies from Unilever Centre for Molecular Informatics to OpenEye]

			==Notes==

			This article heavily reuses content from [http://en.wikipedia.org/wiki/Cheminformatics the Wikipedia article].

			==References==
			<references/>

	[[Category:Informatics]]		[[Category:Informatics]]

Shawndouglas: /* History */ Internal link.

2013-09-13T22:21:09Z

History: Internal link.

← Older revision		Revision as of 22:21, 13 September 2013
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	<blockquote>		<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.		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>		</blockquote>