[Dock-fans] Scoring of hydrophobic interaction!

John J. Irwin jji at cgl.ucsf.edu
Wed May 2 11:19:59 PDT 2007

Hi Gregor

Thanks for your question. I would be surprised if you get a consensus on
this topic, because there are so many variations in the way virtual
screening can be performed, and so many idiosyncrasies of protein
binding sites. I prefer to answer this question by performing
retrospective tests to investigate whether the program & scoring
function can enrich known actives against a database of challenging
decoys with reasonable geometric fidelity compared to available crystal
structures. For example, you can see our paper *Huang, Shoichet and
Irwin, /J. Med. Chem./, 2006, 49(23), 6789-6801.*

Good luck!


Grzegorz Popowicz wrote:
> 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?
> Gregor
> 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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