[Dock-fans] Defining Pharmacophore ?

Tai WANG Tai.Wang at unige.ch
Wed Jan 19 01:57:04 PST 2011

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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