Trent E. Balius
tbalius at aol.com
Thu Aug 10 15:40:37 PDT 2017
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.
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:
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:
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 E. Balius, PhD
Postdoc, Shoichet Lab,
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
From: hom <hom at nmr.umaryland.edu>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Aug 10, 2017 12:21 pm
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.
NMR facility, School of Pharmacy
University of Maryland, Baltimore
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