[Dock-fans] spheres clustering
sudmukh at yahoo.com
Wed May 9 07:29:26 PDT 2007
In general, 48 spheres is a typical number of spheres present in a sphere set. You are not likely to see a major performance benefit by further reducing the number of spheres.
You can convert the 48 spheres to a PDB file using showsphere. Open this PDB file in a visualization program (such a Chimera) to remove the spheres which are too close to each other, and save the PDB file. You can convert this PDB file back to spheres with pdbtosph. Another approach is to write a shell script to do the clustering.
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
----- Original Message ----
From: Yunierkis Perez Castillo <yunierkis at uclv.edu.cu>
To: Scott Brozell <sbrozell at scripps.edu>
Cc: dock-fans at docking.org
Sent: Tuesday, May 8, 2007 1:38:06 PM
Subject: [Dock-fans] spheres clustering
After sphere generation and selection using the distance to an inhibitor present in the crystal structure, I have 48 spheres in my binding site, and all of them are inside the site.
The visual inspection of the spheres shows spheres in the active site very near one to other.
Can I find somewhere any tool to re-cluster these 48 spheres in order to reduce the amount of spheres to use in the docking calculations??.
Thanks in advance
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