Nonlocal electrostatics

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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"/>.
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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.
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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 ==

Revision as of 00:39, 7 July 2011

Nonlocal electrostatics is a technique currently under development which may turn into a powerfull tool for drug design [1] [2] [3].

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

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

  1. Ishizuka, R; Chong, S-H; Hirata, F (2008), "An integral equation theory for inhomogeneous molecular fluids: the reference interaction site model approach.", The Journal of Chemical Physics (AIP) 128 (3): 034504, http://www.ncbi.nlm.nih.gov/pubmed/18205507 
  2. Hildebrandt, A.; Blossey, R.; Rjasanow, S.; Kohlbacher, O.; Lenhof, H.P. (2007), "Electrostatic potentials of proteins in water: a structured continuum approach", Bioinformatics (Oxford Univ Press) 23 (2): e99 
  3. Scott, R.; Boland, M.; Rogale, K.; Fernández, A. (2004), Continuum equations for dielectric response to macro-molecular assemblies at the nano scale, IOP Publishing 
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