[Dock-fans] anchor and rigid docking using 2 anchor points

Trent E. Balius tbalius at aol.com
Wed Jul 21 14:25:49 PDT 2010


 Hi Marsia,

DOCK was not designed to do protein-protein docking.  It is mainly used for docking of small molecules to bio-molecules. 

DOCK will not let some one anchor to segments at the same time but you may grow out from multiple fragments serially to increase sampling. 

See the following section of the manual for discussion of the anchor and grow algorithm.

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility

In our group we have been growing out from multiple anchor fragments with good success.

The parameter "min_anchor_size" defines the size of the ligand fragments. 

min_anchor_size                                              5

Will grow out from all ligands with 5 or more atoms in the fragment.

See the following for example input files:

http://ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Downloads

The flexible docking is the file you should use.

http://george.ams.sunysb.edu/SB2010/FLX.in

With this protocol, 15 rotatable will take on the order of 1 or 2 hours to dock.

30 rotatable bonds may take as long as 12 hours to dock.  

I hope that this helps,   


Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Marsia Gustiananda <marsia at eijkman.go.id>
To: dock-fans at mailman.docking.org
Sent: Wed, Jul 21, 2010 4:38 pm
Subject: [Dock-fans] anchor and rigid docking using 2 anchor points


Hello...

I'm a new dock user.



I've been trying to do macromolecular docking. I tried rigid docking and it 

worked OK (I can regenerate the crystal structure of the complex).  And the 

reason for that I think is because the ligand has been in a right conformation 

for docking.  The ligand is a 9 mer peptide, and the protein is MHC. Then, I 

tried anchor and rigid docking, and this was not successfull. It seems that dock 

choose one anchor point, which is the ring structure in the middle of the 

peptide, and then grow from that point.  According to the literature, residue no 

2 and residue no 9 of the peptide is the anchor points in the peptide-MHC 

complex. My question is: Is it possible to set up two anchor points for anchor 

and rigid docking?  After anchoring, then I need to close the loop between these 

2 anchors.

If so, how do I modify the input file? and what other things necessary to be 

able to do it?



Thank you.



Marsia

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