[Dock-fans] Accessing and applying DOCK6 Scoring Functions

Scott Brozell sbrozell at scripps.edu
Thu Jan 22 15:20:32 PST 2009


Hi,

On Mon, 12 Jan 2009, alexander Zawaira wrote:

>  My name is Alexander Zawaira and I am post-doc researcher based at the University of Cape Town, South Africa.  
>   
> I have started a small project in which I seek to establish the ability of various scoring functions to rank a small set of anti-cancer drugs according to their inhibitory potency against EGFR kinase.  The scoring functions of DOCK6 are an item I am interested-in.  
> 
> I am interested in applying only the scoring functions that come with DOCK6.  I wish to apply the scoring function onto X-ray structures of EGFR Kinase bound to small molecule inhibitors.  Hence, in this application I do NOT wish to perform any actual docking as experimentally determined structures of complexes exist.
> 
>  (a) What are the commands that would allow me to use these scoring functions directly and and (b) what are the file input formats? 
>  

Rescoring is an intended function of DOCK.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Moustakasetal2006

There are example inputs for rescoring in the test suite, eg,
install/test/pbsa_score/pbsa1.dockin
install/test/hawkins_gbsa_score/hawkins_gbsa1.dockin
install/test/continuous_score/continuous1.dockin
install/test/amber_score_1lgu/move_nothing.dockin
etc.

Scott


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