From chemistry-request@ccl.net Wed May 11 07:52:33 2005 Received: from web60213.mail.yahoo.com (web60213.mail.yahoo.com [209.73.178.116]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4BBqTEc016441 for ; Wed, 11 May 2005 07:52:30 -0400 Received: (qmail 96480 invoked by uid 60001); 11 May 2005 10:52:27 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=6A4NAKJXysmJ7hX8FNA0GiRI0cmQtsIwmOHz8UQ8uIANN1EM6da/rfttZSXMpDBcb7wG8ruFdwcgTxmUPpJA9pKO0ZJkajygQTuJgNtKHdzvSBs7CpmKiDj8eVvcK9wCdTB+r+nHCsfHeOowSyoum+/2ohhPl1vG3Fj2iEVUGec= ; Message-ID: <20050511105227.96478.qmail..at..web60213.mail.yahoo.com> Received: from [139.19.34.3] by web60213.mail.yahoo.com via HTTP; Wed, 11 May 2005 03:52:27 PDT Date: Wed, 11 May 2005 03:52:27 -0700 (PDT) From: Its August Subject: Beginner's question on docking To: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net 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