Difference between revisions of "Molecular informatics"
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[[File:BoroPro in dipeptidyl peptidase IV.png|thumb|300px|right|A graphical example of protein-ligand docking using informatics tools]] | [[File:BoroPro in dipeptidyl peptidase IV.png|thumb|300px|right|A graphical example of protein-ligand docking using informatics tools]] | ||
'''Molecular informatics''' is an integrative field of science that examines "chemical and biological data on both the molecular and systemic level" using a wide variety of information technologies.<ref name="BaumannFirst">{{cite journal |url=http://onlinelibrary.wiley.com/doi/10.1002/minf.201190001/full |journal=Molecular Informatics |title=Molecular Informatics - The First Year |author=Baumann, Knut; | '''Molecular informatics''' is an integrative field of science that examines "chemical and biological data on both the molecular and systemic level" using a wide variety of information technologies.<ref name="BaumannFirst">{{cite journal |url=http://onlinelibrary.wiley.com/doi/10.1002/minf.201190001/full |journal=Molecular Informatics |title=Molecular Informatics - The First Year |author=Baumann, Knut; Becker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert |volume=30 |issue=1 |year=January 2011 |page=3 |doi=10.1002/minf.201190001 |accessdate=03 June 2014}}</ref> | ||
Molecular informatics is somewhat related to [[pharmacoinformatics]] in so much as it's used often in the field of drug design and discovery for "lead compound identification, drug target identification, and hit-to-lead optimization."<ref name="BaumannFirst" /><ref name="FlowerDrug">{{cite book |url=http://books.google.com/books?id=Dct237W7pH4C&pg=PA41 |chapter=Molecular Informatics: Sharpening Drug Design's Cutting Edge |title=Drug Design: Cutting Edge Approaches |author=Flower, Darren R. |publisher=Royal Society of Chemistry |pages=1–52 |year=2002 |isbn=9780854048168 |accessdate=03 June 2014}}</ref><ref name="BenderMolSim">{{cite journal |url=http://pubs.rsc.org/en/content/articlelanding/2004/ob/b409813g |journal=Organic & Biomolecular Chemistry |title=Molecular similarity: a key technique in molecular informatics |author=Bender, Andreas; Glen, Robert C. |volume=2 |issue=22 |pages=3204–3218 |year=October 2004 |doi=10.1039/B409813G |accessdate=03 June 2014}}</ref> Other applications include protein-ligand and protein-protein docking as well as biomolecular design. | Molecular informatics is somewhat related to [[pharmacoinformatics]] in so much as it's used often in the field of drug design and discovery for "lead compound identification, drug target identification, and hit-to-lead optimization."<ref name="BaumannFirst" /><ref name="FlowerDrug">{{cite book |url=http://books.google.com/books?id=Dct237W7pH4C&pg=PA41 |chapter=Molecular Informatics: Sharpening Drug Design's Cutting Edge |title=Drug Design: Cutting Edge Approaches |author=Flower, Darren R. |publisher=Royal Society of Chemistry |pages=1–52 |year=2002 |isbn=9780854048168 |accessdate=03 June 2014}}</ref><ref name="BenderMolSim">{{cite journal |url=http://pubs.rsc.org/en/content/articlelanding/2004/ob/b409813g |journal=Organic & Biomolecular Chemistry |title=Molecular similarity: a key technique in molecular informatics |author=Bender, Andreas; Glen, Robert C. |volume=2 |issue=22 |pages=3204–3218 |year=October 2004 |doi=10.1039/B409813G |accessdate=03 June 2014}}</ref> Other applications include protein-ligand and protein-protein docking as well as biomolecular design. | ||
==History== | ==History== | ||
The field of molecular informatics arguably grew out of molecular modeling<ref name="GlenDeveloping">{{cite journal |url=http://pubs.rsc.org/en/content/articlelanding/2002/cc/b207793k |journal=Chemical Communications |title=Developing tools and standards in molecular informatics - Interview by Susan Aldridge |author=Glen, Robert |issue=23 |date=December 2002 |pages=2745–2747 |doi=10.1039/B207793K |accessdate=03 June 2014}}</ref><ref name="KorkinNewMod">{{cite book |url=http://dl.acm.org/citation.cfm?id=1087511 |title=A New Model for Molecular Representation and Classification: Formal Approach Based on the ETS Framework |author=Korkin, Dmitry |publisher=University of New Brunswick Fredericton |year=2003 |pages=652 |isbn=0612988686 |accessdate=03 June 2014}}</ref><ref name="BaumannMI">{{cite journal |url=http://onlinelibrary.wiley.com/doi/10.1002/minf.201290001/full |journal=Molecular Informatics |title=Molecular Informatics - A Leading Discipline in a Complex Emerging Field |author=Baumann, Knut; Ecker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert |volume=31 |issue=1 |year=January 2012 |page=3 |doi=10.1002/minf.201290001 |accessdate=03 June 2014}}</ref>, a tool of [[Chemical informatics|chemoinformatics]] that uses theoretical methods and computational techniques to replicate the behavior of molecules, often as a three-dimensional representation. Gradually, the fields of biology, chemistry, and [[Informatics (academic field)|informatics]] began to integrate, as the editors of the journal ''Molecular Informatics'' noted in a 2012 editorial: | The field of molecular informatics arguably grew out of molecular modeling<ref name="GlenDeveloping">{{cite journal |url=http://pubs.rsc.org/en/content/articlelanding/2002/cc/b207793k |journal=Chemical Communications |title=Developing tools and standards in molecular informatics - Interview by Susan Aldridge |author=Glen, Robert |issue=23 |date=December 2002 |pages=2745–2747 |doi=10.1039/B207793K |accessdate=03 June 2014}}</ref><ref name="KorkinNewMod">{{cite book |url=http://dl.acm.org/citation.cfm?id=1087511 |title=A New Model for Molecular Representation and Classification: Formal Approach Based on the ETS Framework |author=Korkin, Dmitry |publisher=University of New Brunswick Fredericton |year=2003 |pages=652 |isbn=0612988686 |accessdate=03 June 2014}}</ref><ref name="BaumannMI">{{cite journal |url=http://onlinelibrary.wiley.com/doi/10.1002/minf.201290001/full |journal=Molecular Informatics |title=Molecular Informatics - A Leading Discipline in a Complex Emerging Field |author=Baumann, Knut; Ecker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert |volume=31 |issue=1 |year=January 2012 |page=3 |doi=10.1002/minf.201290001 |accessdate=03 June 2014}}</ref>, a tool of [[Chemical informatics|chemoinformatics]] that uses theoretical methods and computational techniques to replicate the behavior of molecules, often as a three-dimensional representation. Gradually, the fields of biology, chemistry, and [[Informatics (academic field)|informatics]] began to integrate, as the editors of the journal ''Molecular Informatics'' noted in a 2012 editorial: | ||
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As informatics and molecular modeling began playing a more important role in chemical and biological research, the fields of [[bioinformatics]] and chemoinformatics emerged, with the concept of molecular informatics in turn forming around them.<ref name="BaumannMI" /><ref name="FlowerDrug" /><ref name="ErikksonMulti">{{cite book |url=http://books.google.com/books?id=2CHrDa-kBSYC&pg=PA85 |chapter=Chapter 21: Chem- and Bioinformatics |title=Multi- and Megavariate Data Analysis, Part 2, Advanced Applications and Method Extensions |author=Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Trygg, J.; Wikström, C.; Wold, S. |publisher=MKS Umetrics AB |pages=85–97 |year=2006 |isbn=9789197373036}}</ref> | As informatics and molecular modeling began playing a more important role in chemical and biological research, the fields of [[bioinformatics]] and chemoinformatics emerged, with the concept of molecular informatics in turn forming around them.<ref name="BaumannMI" /><ref name="FlowerDrug" /><ref name="ErikksonMulti">{{cite book |url=http://books.google.com/books?id=2CHrDa-kBSYC&pg=PA85 |chapter=Chapter 21: Chem- and Bioinformatics |title=Multi- and Megavariate Data Analysis, Part 2, Advanced Applications and Method Extensions |author=Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Trygg, J.; Wikström, C.; Wold, S. |publisher=MKS Umetrics AB |pages=85–97 |year=2006 |isbn=9789197373036}}</ref> | ||
==Application== | |||
Molecular informatics can help tackle problems and tasks such as the following<ref name="BaumannFirst" /><ref name="BaumannMI" /><ref name="BenderMol">{{cite web |url=http://pubs.rsc.org/en/Content/ArticleLanding/2004/OB/b409813g#!divAbstract |title=Molecular similarity: a key technique in molecular informatics |journal=Organic & Biomolecular Chemistry |author=Bender, Andreas; Glen, Robert C. |volume=2 |issue=22 |pages=3204–3218 |year=November 2004 |pmid=15534697 |doi=10.1039/B409813G}}</ref><ref name="BaumannBD">{{cite web |url=http://onlinelibrary.wiley.com/doi/10.1002/minf.201580131/full |title=Systems Approaches and Big Data in Molecular Informatics |journal=Molecular Informantics |author=Baumann, Knut; Becker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert |volume=34 |issue=1 |pages=2 |year=January 2015 |doi=10.1002/minf.201580131}}</ref>: | |||
* documenting and studying protein-ligand and protein-protein docking | |||
* designing, studying, and identifying pharmaceutical solutions for health problems | |||
* identifying "genetic and epigenetic signals related to diseases" | |||
* calculating chemical properties of molecular and sub-molecular interactions | |||
* mining small molecule and drug target databases | |||
* using machine learning techniques to generate models of candidate molecule properties | |||
* grouping molecules into practical divisions by biological and physicochemical properties | |||
==Informatics== | |||
With the advent of "Big Data," molecular informatics is turning to machine-learning tools for predictive modeling, improved 3-D visualization tools for analyzing molecular structure and function, and system-wide approaches to experimental procedures.<ref name="BaumannBD" / > | |||
==Further reading== | |||
* {{cite web |url=http://physchem.org.uk/Symp05/0_glen_physchemforum5.pdf |format=PDF |author=Glen, Robert C. |title=Molecular Informatics: A finger in every pie |publisher=PhysChem Forum - 5th Symposium |date=18 June 2008}} | |||
==External links== | |||
==References== | ==References== | ||
Revision as of 20:32, 31 March 2015
Molecular informatics is an integrative field of science that examines "chemical and biological data on both the molecular and systemic level" using a wide variety of information technologies.[1]
Molecular informatics is somewhat related to pharmacoinformatics in so much as it's used often in the field of drug design and discovery for "lead compound identification, drug target identification, and hit-to-lead optimization."[1][2][3] Other applications include protein-ligand and protein-protein docking as well as biomolecular design.
History
The field of molecular informatics arguably grew out of molecular modeling[4][5][6], a tool of chemoinformatics that uses theoretical methods and computational techniques to replicate the behavior of molecules, often as a three-dimensional representation. Gradually, the fields of biology, chemistry, and informatics began to integrate, as the editors of the journal Molecular Informatics noted in a 2012 editorial:
"Later on, when the few protein structures available could be analysed with the first graphical molecular modelling packages, the automated docking of ligands into the binding cavities of proteins offered a means to generate hypotheses of protein-ligand interactions at the atomic level. These were exciting times for some of the chemists and biologists that envisaged the wealth of opportunities that integrating informatics into those traditional disciplines could offer for gaining a deeper understanding, but also widening the scope, of how small molecules interact with macromolecules."[6]
As informatics and molecular modeling began playing a more important role in chemical and biological research, the fields of bioinformatics and chemoinformatics emerged, with the concept of molecular informatics in turn forming around them.[6][2][7]
Application
Molecular informatics can help tackle problems and tasks such as the following[1][6][8][9]:
- documenting and studying protein-ligand and protein-protein docking
- designing, studying, and identifying pharmaceutical solutions for health problems
- identifying "genetic and epigenetic signals related to diseases"
- calculating chemical properties of molecular and sub-molecular interactions
- mining small molecule and drug target databases
- using machine learning techniques to generate models of candidate molecule properties
- grouping molecules into practical divisions by biological and physicochemical properties
Informatics
With the advent of "Big Data," molecular informatics is turning to machine-learning tools for predictive modeling, improved 3-D visualization tools for analyzing molecular structure and function, and system-wide approaches to experimental procedures.<ref name="BaumannBD" / >
Further reading
- Glen, Robert C. (18 June 2008). "Molecular Informatics: A finger in every pie" (PDF). PhysChem Forum - 5th Symposium. http://physchem.org.uk/Symp05/0_glen_physchemforum5.pdf.
External links
References
- ↑ 1.0 1.1 1.2 Baumann, Knut; Becker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert (January 2011). "Molecular Informatics - The First Year". Molecular Informatics 30 (1): 3. doi:10.1002/minf.201190001. http://onlinelibrary.wiley.com/doi/10.1002/minf.201190001/full. Retrieved 03 June 2014.
- ↑ 2.0 2.1 Flower, Darren R. (2002). "Molecular Informatics: Sharpening Drug Design's Cutting Edge". Drug Design: Cutting Edge Approaches. Royal Society of Chemistry. pp. 1–52. ISBN 9780854048168. http://books.google.com/books?id=Dct237W7pH4C&pg=PA41. Retrieved 03 June 2014.
- ↑ Bender, Andreas; Glen, Robert C. (October 2004). "Molecular similarity: a key technique in molecular informatics". Organic & Biomolecular Chemistry 2 (22): 3204–3218. doi:10.1039/B409813G. http://pubs.rsc.org/en/content/articlelanding/2004/ob/b409813g. Retrieved 03 June 2014.
- ↑ Glen, Robert (December 2002). "Developing tools and standards in molecular informatics - Interview by Susan Aldridge". Chemical Communications (23): 2745–2747. doi:10.1039/B207793K. http://pubs.rsc.org/en/content/articlelanding/2002/cc/b207793k. Retrieved 03 June 2014.
- ↑ Korkin, Dmitry (2003). A New Model for Molecular Representation and Classification: Formal Approach Based on the ETS Framework. University of New Brunswick Fredericton. pp. 652. ISBN 0612988686. http://dl.acm.org/citation.cfm?id=1087511. Retrieved 03 June 2014.
- ↑ 6.0 6.1 6.2 6.3 Baumann, Knut; Ecker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert (January 2012). "Molecular Informatics - A Leading Discipline in a Complex Emerging Field". Molecular Informatics 31 (1): 3. doi:10.1002/minf.201290001. http://onlinelibrary.wiley.com/doi/10.1002/minf.201290001/full. Retrieved 03 June 2014.
- ↑ Eriksson, L.; Johansson, E.; Kettaneh-Wold, N.; Trygg, J.; Wikström, C.; Wold, S. (2006). "Chapter 21: Chem- and Bioinformatics". Multi- and Megavariate Data Analysis, Part 2, Advanced Applications and Method Extensions. MKS Umetrics AB. pp. 85–97. ISBN 9789197373036. http://books.google.com/books?id=2CHrDa-kBSYC&pg=PA85.
- ↑ Bender, Andreas; Glen, Robert C. (November 2004). "Molecular similarity: a key technique in molecular informatics". pp. 3204–3218. doi:10.1039/B409813G. PMID 15534697. http://pubs.rsc.org/en/Content/ArticleLanding/2004/OB/b409813g#!divAbstract.
- ↑ Baumann, Knut; Becker, Gerhard F.; Mestres, Jordi; Schneider, Gisbert (January 2015). "Systems Approaches and Big Data in Molecular Informatics". pp. 2. doi:10.1002/minf.201580131. http://onlinelibrary.wiley.com/doi/10.1002/minf.201580131/full.
