From chemistry-request@ccl.net Wed May 11 18:02:26 2005 Received: from mx.seanet.com (mx.seanet.com [199.181.164.10] (may be forged)) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4BM2Jgp027318 for ; Wed, 11 May 2005 18:02:22 -0400 Received: from planaria (c-24-18-186-63.hsd1.wa.comcast.net [24.18.186.63]) (authenticated bits=0) by milkyway.seanet.com (8.13.2/8.13.2) with ESMTP id j4BM2ACK018806; Wed, 11 May 2005 15:02:18 -0700 (PDT) (envelope-from mark %a% arguslab.com) Reply-To: From: "Mark Thompson" To: "Its August" , Subject: RE: Beginner's question on docking Date: Wed, 11 May 2005 15:02:13 -0700 Message-ID: <000401c55675$16725080$0200a8c0@planaria> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 In-Reply-To: <20050511105227.96478.qmail %a% web60213.mail.yahoo.com> Importance: Normal X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net You should read "Automated docking using a Lamarckian Genetic Algorithm,....." by Morris, Goodsell, Olson, et. al. J. Comp. Chem. 19, 1639-1662, (1998) It will answer several of your questions. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request %a% ccl.net]On Behalf Of Its August Sent: Wednesday, May 11, 2005 3:52 AM To: chemistry %a% ccl.net Subject: CCL:Beginner's question on docking Hello, I've two question on ligand docking. Excuse me for asking such very basic questions: 1. Docking methods calculate Binding Free Energy differences( or Delta G) as a measure of binding Affinity.(Please correct me if I'm wrong). Is there any other Thermodynamic function that can replace Delta G as a measure of binding affinity for ? 2. On Docking in a Grid: Docking programs like AUTODOCK evalutae the Energy of a molecule on a GRID. I beleive the a GRID point is nothing but a point in a 3d Space for which u know the binding affinity of a particular chemical group precomputed at that GRID point. However in some pose of the ligands one particular chemical group MAY NOT EXACTLY fall in one of such GRID point(Whatever fine resolution the grid may have ) How to calcualte energy in that case? I've came across a term like GRID INTERPOLATION. Is that anything to do with in such a case? Moreover I would like to know how additive are these interactions. That means the energy computed for an isolated chemical group in a GRID , is it equal for the same group in a ligand or in a set of different ligands? Do the other neighbouring chemical groups exert some effect? Are there any literature references for this? Thanks in advance Discover Yahoo! Find restaurants, movies, travel and more fun for the weekend. Check it out! http://discover.yahoo.com/weekend.html -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY %a% ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST %a% ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+