[Dock-fans] Defining Pharmacophore ?

Trent E. Balius tbalius at aol.com
Sun Jan 23 11:15:16 PST 2011

 Hi Tai,

This functionality is not currently in dock 6.4.  However the Rizzo group is developing a method that may be of interest to you and will be released in a future version of dock.  We termed it Footprint Similarity score and we have just submitted a paper on this re-scoring method to J Comput Chem.

Take care, 



-----Original Message-----
From: Tai WANG <Tai.Wang at unige.ch>
To: dock-fans at mailman.docking.org
Sent: Wed, Jan 19, 2011 4:57 am
Subject: [Dock-fans] Defining Pharmacophore ?

Dear Dock6 team,

I'm working on virtual screening project on a protein with defined ATP binding 

pocket. From established knowledge we know that some residues in the bottom of 

the pocket  play as crucial pharmacophores (H-acceptor) for effective 

ligand/inhibitor binding. However most of the high-scored hits we got (using 

default parameter) from dock6 have nice shape fitting (hydrophobic interaction) 

in the pocket but do not interact by H-bond with those known pharmacophores, 

which seems to be normal because the hydrophobic interaction may surpass the 

importance of H-bonds in grid score. 

My question is whether the Dock6 has the functions to take account of H-bond 

with manually defined pharmacophores? Or to filter the hits that don't interact 

on H-bond with defined pharmacophores (residues)? 

Thank for your response. And please forgive for any stupid question since I'm 

just a beginner of the program.



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