From chemistry-request@server.ccl.net Wed May 22 15:50:12 2002 Received: from s31xu1.systems.smu.edu ([129.119.70.85]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4MJoC006814 for ; Wed, 22 May 2002 15:50:12 -0400 Received: by s31xu1.systems.smu.edu with Internet Mail Service (5.5.2655.55) id ; Wed, 22 May 2002 14:50:09 -0500 Message-ID: From: "Henkes, Amanda Erin" To: "'chemistry@ccl.net'" Subject: Docking Ligands using FlexX Date: Wed, 22 May 2002 14:50:01 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: text/plain I am using Sybyl FlexX. I downloaded the protein 1A7T from the Protein Data Bank (www.rcsb.org). It is called Metallo-B-Lactamase with the ligand MES docked into it. When trying to reproduce the experimental results of docking MES into the active site, containing ZN251 and ZN252, FlexX orients the ligand with the SO3 group oriented towards the two zincs. But, the experimentally docked ligand of MES has the SO3 group oriented towards the N of the LYS167 group. I tried including the LYS167 as part of the active site, but this did not change the orientation of the docked ligand. What forces cause the ligand to orient with the SO3 group near the LYS167? How can I use FlexX to duplicate this experimental data? Amanda Henkes Southern Methodist University aehenkes@mail.smu.edu