[Dock-fans] dock_6.8

Trent E. Balius tbalius at aol.com
Thu Aug 10 15:40:37 PDT 2017


 Hi Kellie,

Yes.  

I assume that you have a structure of the receptor.  Is that right?

(1) Identify the site where you believe that the molecule binds.  
(2) select a central residue and save just that residue as a mol2 (alternatively you could calculate center of mass of a bunch of residues).  
(3)  find the spheres that are close to that residue.  

Follow the following tutorial.  

http://ringo.ams.stonybrook.edu/index.php/2017_DOCK_tutorial_1_with_PDB_4QMZ_NEW

Use the central residue file instead of the ligand file.

 >> sphere_selector rec.sph ../01.dockprep/central_res.mol2 6.0

You could use the GRID based footprint scoring function:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#MultiGridScore

Here are some useful parameter:

 multigrid_score_weights_text [no] (yes no): 
          #Flag for providing a textfile as input for the reference footprint.

 multigrid_score_footprint_text [reference.txt] (): 
            #Name of the reference footprint input text file. 

Set these parameters as follows:  
  multigrid_score_weights_text  yes
  multigrid_score_footprint_text reference.txt

You will need to define the strength of the interaction by hand.   

I am also sending this to dock-fans mailing list.

I hope that this helps,

Trent

======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: hom <hom at nmr.umaryland.edu>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Aug 10, 2017 12:21 pm
Subject: dock_6.8

Dr. Balius,
I am wondering if you could point me to find a protocol for docking of 
small molecules to protein, without a crystal structure of the 
complex, but by using NMR data as a guide to define the binding 
interaction.  I have chemical shift perturbation data for the protein upon 
binding to compound x and saturation-transfer data on compound x when 
bound to the protein.  We have a series of related compounds, and want to 
see if we could use dock (perhaps making use of the footprint scoring?) to 
help with drug design.  Thank you in advance.

Kellie Hom
NMR facility, School of Pharmacy
University of Maryland, Baltimore


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