From chemistry-request@ccl.net Tue Nov 4 08:58:04 2003 Received: from smtp02.syd.iprimus.net.au (smtp02.syd.iprimus.net.au [210.50.76.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA4DvVhP013643 for ; Tue, 4 Nov 2003 08:57:32 -0500 Received: from alex.roach (210.50.176.121) by smtp02.syd.iprimus.net.au (7.0.020) id 3F8F522A005DB58F for chemistry$at$ccl.net; Wed, 5 Nov 2003 00:57:30 +1100 Received: from alex by alex.roach with local (Exim 3.35 #1 (Debian)) id 1AH1oD-0007GO-00 for ; Wed, 05 Nov 2003 01:05:25 +1100 Date: Wed, 5 Nov 2003 01:05:24 +1100 To: chemistry$at$ccl.net Subject: blind docking of large protein molecules Message-ID: <20031104140524.GA27892@alex> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i From: Alex Sutcliffe X-Spam-Status: No, hits=-2.5 required=7.0 tests=USER_AGENT_MUTT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I am interested in investigating potential dockings between protein molecules and only have pretty limited ideas about potential binding sites. I have toyed with autodock, zdock and hex with mixed results and am finding it a bit intensive resources wise. What packages or combinations there of do people recommend for this sort of thing? Since it does not seem feasible attempt to use both molecules in their entirety, I was thinking about splitting one into smaller chunks, ie grabbing chunks that are close to the surface and attempting to dock them in turn. Does anyone have any experience or tips from similar efforts or know of any papers etc detailing any efforts or methodologies that I might find useful? Thanks in advance! Alex Sutcliffe