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 MW<250Da. 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
