Hi Simon,
I suggest docking with the free web service DockBlaster:
http://blaster.docking.org/start.shtml
DockBlaster runs DOCK 3.5.54 and gives you the freedom to dock any molecule
you want into your structure.
Check out this page for more information:
http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_Blaster:FAQ
All you need is a PDB file as input. After the preparation step, you can
choose what library you want to dock. A library of interest for you is the
fragment-like molecule library of ZINC (http://zinc.docking.org). Currently,
it contains 458080 purchasable molecules with MW250Da.
It should be docked within a couple of days and and give you an idea what
kind of molecules might fit into your pocket.
Good luck,
Oliv
On Wed, Jan 6, 2010 at 5:08 AM, Simon Kolstoe s.kols...@ucl.ac.uk wrote:
Dear ccp4bb
A structure I have recently finished has a cavity with four waters in it. I
am wondering if I might be able to fit a small molecule in the same place.
Does anyone know a way of making some type of map of this cavity and then
searching through a small molecule library to see what might fit in it (I'm
guessing there is commercial software that will do this however I am after
something without large financial commitments!)?
Thanks,
Simon
--
Oliv Eidam, Ph.D.
Postdoctoral fellow
University of California, San Francisco
Dept. of Pharmaceutical Chemistry
1700 4th Street, Byers Hall North, Room 501
San Francisco, CA 94158 - Box 2550
Phone: 415-514-4253
Fax : 415-514-4260
Email: eid...@blur.compbio.ucsf.edu
