From owner-chemistry*- at -*ccl.net Fri Feb 26 18:01:00 2016 From: "Scott Brozell srb|osc.edu" To: CCL Subject: CCL: Can Dock6.7 predict binding site? Message-Id: <-52058-160226175746-18530-QTSK6M3f/1F8NgNs+FMNPg===server.ccl.net> X-Original-From: Scott Brozell Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 26 Feb 2016 17:57:36 -0500 Mime-Version: 1.0 Sent to CCL by: Scott Brozell [srb^osc.edu] Hi, Short answers to your questions are 1. you identified the binding region(s); this could have been a single specific site or the whole receptor; see this tutorial for the recipe: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm 2. Dock can be used to predict binding sites, but that is not its main intended purpose nor a particular strength. 3. Dock's main focus is receptor-ligand complexes. Novel uses have been made in the past. For some more detail about binding site selection, see the response on the Dock mailing list: http://mailman.docking.org/pipermail/dock-fans/2016-February/003150.html For an overview of Dock, see http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm scott On Thu, Feb 25, 2016 at 02:31:12AM -0500, Syeda Sumayya Tariq sumayyatariq7**gmail. com wrote: > > I have recently started working with Dock6.7 and have a little query. > The issue is I have used Dock6.7 to dock a receptor protein with a small > molecule I retrieved from a database. The receptor site where docking > occurred shows some of the residues SAME as were predicted CPORT which is > responsible for predicting active residues. > My question is how did Dock identify the binding site? Is it by chance or > is Dock able to predict binding site also? Is it true that Dock can only > work with a receptor-ligand complex?