[Dock-fans] Scoring of hydrophobic interaction!

Grzegorz Popowicz popowicz at biochem.mpg.de
Fri Sep 13 16:26:38 PDT 2002

Dear All,
I am trying to screen for a ligand which will bind to a fully hydrophobic 
cleft of my protein. What scoring algorithm is considered/believed the best 
for this purpose?


On Wednesday 02 May 2007 09:47, Carsten Baldauf wrote:
> Dear All,
> There will be a workshop on problems of molecular docking and
> applications of sophisticated optimization algorithms held as a
> satellite conference of the European Conference on Complex Systems in
> October 2007 in Dresden.
> The molecular docking problem is to find the best orientation of two
> molecules to each other. The interaction can be modeled by a scoring
> function that includes terms describing the inter- and intramolecular
> energies. The number of degrees of freedom strongly depends on the
> complexity of the docking approach. The resulting fitness landscape is
> highly irregular. Due to this complexity sophisticated optimization
> algorithms are needed. Bio-inspired methods are known to be valuable
> tools to successfully explore such search spaces.In order to gain a
> deeper insight to biochemical processes and to support the finding of
> potent drugs, these methods are of great importance in academic and
> industrial research.
> The aim of the workshop is to serve as platform for scientific exchange
> and collaboration.
> There will be six session on the topics:
> - Modeling of molecular interaction
> - High throughput screening and clustering
> - Protein-Protein Docking
> - Bio-inspired optimization
> - Fitness landscapes
> - Multi-objective approaches
> Besides invited talks, there are free slots for presentations and the
> possibility to hang a poster. Applications for presentations from
> researchers at the pre/post-doctoral level are especially encouraged.
> Links:
> For the workshop see http://pacosy.informatik.uni-leipzig.de/MDCO-2007
> For the ECCS'07 see http://www.trafficforum.org/dresden
> Please spread this E-mail in your communities!
> Thank you and best wishes from Dresden,
> Carsten Baldauf
> --
> dr carsten baldauf
> biotechnologisches zentrum der tu dresden
> http://www.biotec.tu-dresden.de/pisabarro
> http://www.biotec.tu-dresden.de/~carstenb
> Molecular Docking, Complexity, and Optimization
> See http://pacosy.informatik.uni-leipzig.de/MDCO-2007/
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
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