From chemistry-request@ccl.net Sun Dec 21 18:25:58 2003 Received: from smtp3.unsw.edu.au (smtp3.unsw.EDU.AU [149.171.96.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBLNPOHt029152 for ; Sun, 21 Dec 2003 18:25:26 -0500 Received: from localhost (antivirus-04.services.comms.unsw.EDU.AU [149.171.193.83]) by smtp3.unsw.edu.au (8.11.2/8.11.2) with ESMTP id hBLNPNB12465 for ; Mon, 22 Dec 2003 10:25:23 +1100 (EST) Received: from iprimus.com.au ([129.94.63.237]) by smtp.unsw.edu.au (8.11.2/8.11.2) with ESMTP id hBLNPLB12388 for ; Mon, 22 Dec 2003 10:25:22 +1100 (EST) Message-ID: <3FE628C1.5080604[at]iprimus.com.au> Date: Mon, 22 Dec 2003 10:12:01 +1100 From: Alex Sutcliffe User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20030502 Debian/1.2.1-9woody3 X-Accept-Language: en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: rebuilding a molecule after changing the coordinates of a subsection Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I have a molecule in pdb format. I have chopped out a fragment and tried docking it to another molecule. So now I have new coordinates for just the subsection. I would like to be able to rebuild the rest of the molecule in relation to the new coordinates. Any suggestions on the best way to do this? Thanks Alex From chemistry-request@ccl.net Sun Dec 21 23:01:47 2003 Received: from uis-gumail-2.georgetown.edu (postoffice-2.georgetown.edu [141.161.1.110]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBM41FHt008751 for ; Sun, 21 Dec 2003 23:01:15 -0500 Received: from imap.georgetown.edu (uis-gumail-5.georgetown.edu [141.161.88.141]) by uis-gumail-2.georgetown.edu (8.12.10/8.12.10) with ESMTP id hBM40UT1006392 for ; Sun, 21 Dec 2003 23:01:15 -0500 (EST) Received: from [128.8.23.139] by imap.georgetown.edu (mshttpd); Sun, 21 Dec 2003 23:00:30 -0500 From: Sivanesan Dakshanamurthy To: chemistry|at|ccl.net Message-ID: <463fe45b23.45b23463fe|at|imap.georgetown.edu> Date: Sun, 21 Dec 2003 23:00:30 -0500 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: FlexX Docking X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-GU-FilterVersion: 1.22 X-Scanned-By: MIMEDefang 2.36 X-Spam-Status: No, hits=0.6 required=7.0 tests=FROM_ENDS_IN_NUMS,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear ALL; I was doing docking of database contains several tested in vitro/vivo compounds with a specific crystal structure using FLEXX. I gave crystal structure ligand as reference ligand for docking purpose. At the same time, database contains native ligand as well as their analogs. I computed CSCORE including drug score apart from flex score. At this point, From the docking result one may have to expect that the native ligand should be top scored. But when I sort various scoring functions; I may not be able to get native ligand docked in top 100 according to scoring functions. Could anybody explain the reason, why docking may not be able to reproduce the native ligand in the thier structure. I would deeply appreciate your reply, Thanks in advance Sivanesan D.Sivanesan, Ph.D. Dept. of Oncology, Lombardi Cancer Center (NCI Comprehensive Cancer Center), Georgetown University, DC 20057 Phone: 202-687-6338