[Dock-fans] spheres clustering

Sudipto Mukherjee sudmukh at yahoo.com
Wed May 9 07:29:26 PDT 2007


Hi Yunierkis,

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. 
 
Regards
Sudipto Mukherjee
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




  
  

Hi all.



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

Yunierkis
Servicio de Correos del Grupo de Redes. UCLV 
Participe en Universidad 2008 del 11 al 15 de febrero del 2008.
Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu
_______________________________________________
Dock-fans mailing list
Dock-fans at docking.org
http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans






__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070509/e552e8c5/attachment.html


More information about the Dock-fans mailing list