[Dock-fans] Short contact in ligand

Rahul Banerjee rahul.banerjee at chemistry.msu.edu
Wed May 27 09:04:50 PDT 2009


Hi,

Sometimes I am getting very strange geometries of the ligand in Dock run. Two groups or atoms in the ligand are in short contact. Cases are even worst if I use use_clash_overlap . If I don't use use_clash_overlap there is marginal improvement. Is there any other option I can use to get rid of these highly strained ligand conformations? I am using grid based scoring to screen big databases. I some cases ligands with these type of strained geometries are appearing among top ranked compounds.

With best regards,
Rahul Banerjee


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