ADL: docking results not very accurate

Fabian Glaser fglaser at
Thu Jan 31 00:40:24 PST 2008

Dear Autodock colleagues,

I'd be very grateful for any advice with the following:

I am trying to perform docking experiments for a colleague. Initially I 
have performed several experiments trying to re-dock the co-crystallized 
ligand (the structure is 1nex, and the ligand, a modified peptide), to 
check the procedure, and later the idea is to use the same procedure to 
dock a peptide that they think represents the substrate on a modelled 

The problem is that when I try to dock the co-crystallized ligand (as an 
initial test), the "correct" result does not appear in the best energy 
cluster: Attached figure snapshot3.png shows the best energetic cluster 
found within 100 docked results, and snapshot2.png the second best 
cluster, which is the correct  one (in blue the protein, in green the 
co-crystallized ligand, the docked ligand is colored by element). The 
different clusters are shown in the small figure on the right, in blue 

I am quite a rocky with docking, so any help how can I improve these 
results will be highly appreciated.

Best regards and thanks a lot in advance.


Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

E-mail: fglaser at
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396


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