Nonlocal electrostatics - Revision history

imported>Luis at 21:26, 13 February 2012

2012-02-13T21:26:06Z

← Older revision		Revision as of 16:26, 13 February 2012
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	Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.		Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.

	~~The idea~~ is that ~~when computing~~ the electric potential around a protein, ~~which is~~ surrounded by water~~, this~~ potential interacts with the ions in the water. The ions change the orientation, which affects the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a more accurate model to predict protein docking (if two proteins will stuck together). When trying to find a drug which would interact with certain protein, the first step is to look for a molecule which will stick to the desired protein, and that is when this methods become very useful.		Finding a drug for a specific purpose is without a doubt a very difficult task, and today it is largely a trial and error experimental process. A first screening that could simplify the process would be to automatically detect which molecules will stick to certain proteins. This effect is called ''protein docking''. If a molecule sticks to a protein, it is certainly more likely to affect it. In theory one can numerically compute the electric potential around a protein to see if it matches the corresponding potential generated by the molecule. If done naively, the predicted results do not coincide with the experiments. The underlying reason seems to be that the large molecules are surrounded by liquid, mostly water. Their potential interacts with the ions in the water. The ions change the orientation, which affects the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a more accurate model to predict protein docking.

	== Links ==		== Links ==

imported>Nestor at 06:00, 7 February 2012

2012-02-07T06:00:15Z

← Older revision		Revision as of 01:00, 7 February 2012
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	== Links ==		== Links ==
	There is a group in the center for Bioinformatics in Saarland University doing research in this field actively. They have a webside describing the project		There is a group in the center for Bioinformatics in Saarland University doing research in this field actively. They have a webside describing the project
	http://bioinf-www.bioinf.uni-sb.de/projects/solvation		http://bioinf-www.bioinf.uni-sb.de/projects/solvation.html

	== References ==		== References ==

imported>Luis at 02:34, 6 February 2012

2012-02-06T02:34:37Z

← Older revision		Revision as of 21:34, 5 February 2012
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	<ref name="SBRF">{{Citation \| last1=Scott \| first1=R. \| last2=Boland \| first2=M. \| last3=Rogale \| first3=K. \| last4=Fernández \| first4=A. \| title=Continuum equations for dielectric response to macro-molecular assemblies at the nano scale \| publisher=IOP Publishing \| year=2004}}</ref>		<ref name="SBRF">{{Citation \| last1=Scott \| first1=R. \| last2=Boland \| first2=M. \| last3=Rogale \| first3=K. \| last4=Fernández \| first4=A. \| title=Continuum equations for dielectric response to macro-molecular assemblies at the nano scale \| publisher=IOP Publishing \| year=2004}}</ref>
	}}		}}


			{{stub}}

imported>Luis at 16:53, 23 January 2012

2012-01-23T16:53:10Z

← Older revision		Revision as of 11:53, 23 January 2012
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	Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.		Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.

	The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water, which ~~affect~~ the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a ~~much~~ more accurate model to predict protein docking (if two proteins will stuck together). When trying to find drug which would interact with certain protein, the first step is to look for a molecule which will stick to the desired protein, and that is when this methods become very useful.		The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water. The ions change the orientation, which affects the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a more accurate model to predict protein docking (if two proteins will stuck together). When trying to find a drug which would interact with certain protein, the first step is to look for a molecule which will stick to the desired protein, and that is when this methods become very useful.

	== Links ==		== Links ==

imported>Luis at 00:40, 7 July 2011

2011-07-07T00:40:16Z

← Older revision		Revision as of 19:40, 6 July 2011
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	Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.		Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.

	The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water, which affect the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a much more accurate model to predict protein docking (if two proteins will stuck together). When trying to find drug which would interact with certain protein, the first step is to look for molecule which will stick to the desired protein, and that is when this methods become very useful.		The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water, which affect the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a much more accurate model to predict protein docking (if two proteins will stuck together). When trying to find drug which would interact with certain protein, the first step is to look for a molecule which will stick to the desired protein, and that is when this methods become very useful.

	== Links ==		== Links ==

imported>Luis at 00:39, 7 July 2011

2011-07-07T00:39:55Z

← Older revision		Revision as of 19:39, 6 July 2011
Line 1:		Line 1:
	Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.		Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.

	The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water, which affect the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a much more accurate model to predict protein docking (if two proteins will stuck together). When ~~seeking~~ drug which would interact with certain protein, the first step is to look for molecule which will stick to the desired protein, and that is when this methods become very useful.		The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water, which affect the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a much more accurate model to predict protein docking (if two proteins will stuck together). When trying to find drug which would interact with certain protein, the first step is to look for molecule which will stick to the desired protein, and that is when this methods become very useful.

	== Links ==		== Links ==

imported>Luis: Created page with "Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design . ..."

2011-07-07T00:04:50Z

Created page with "Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>. ..."

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Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design <ref name="ICH"/> <ref name="HBRK"/> <ref name="SBRF"/>.

The idea is that when computing the electric potential around a protein, which is surrounded by water, this potential interacts with the ions in the water, which affect the potential effectively transforming it from the classical coulomb potential (i.e. the fundamental solution of the Laplacian) to the potential of an integral operator (the fractional Laplacian in the simplest case). Experimentally, this has shown to provide a much more accurate model to predict protein docking (if two proteins will stuck together). When seeking drug which would interact with certain protein, the first step is to look for molecule which will stick to the desired protein, and that is when this methods become very useful.

== Links ==
There is a group in the center for Bioinformatics in Saarland University doing research in this field actively. They have a webside describing the project
http://bioinf-www.bioinf.uni-sb.de/projects/solvation

== References ==
{{reflist|refs=
<ref name="ICH">{{Citation | last1=Ishizuka | first1=R | last2=Chong | first2=S-H | last3=Hirata | first3=F | title=An integral equation theory for inhomogeneous molecular fluids: the reference interaction site model approach. | url=http://www.ncbi.nlm.nih.gov/pubmed/18205507 | publisher=AIP | year=2008 | journal=The Journal of Chemical Physics | volume=128 | issue=3 | pages=034504}}</ref>
<ref name="HBRK">{{Citation | last1=Hildebrandt | first1=A. | last2=Blossey | first2=R. | last3=Rjasanow | first3=S. | last4=Kohlbacher | first4=O. | last5=Lenhof | first5=H.P. | title=Electrostatic potentials of proteins in water: a structured continuum approach | publisher=Oxford Univ Press | year=2007 | journal=Bioinformatics | volume=23 | issue=2 | pages=e99}}</ref>
<ref name="SBRF">{{Citation | last1=Scott | first1=R. | last2=Boland | first2=M. | last3=Rogale | first3=K. | last4=Fernández | first4=A. | title=Continuum equations for dielectric response to macro-molecular assemblies at the nano scale | publisher=IOP Publishing | year=2004}}</ref>
}}