From owner-chemistry@ccl.net Fri Jul 11 03:16:01 2008 From: "Vidana.Epa .. csiro.au" To: CCL Subject: CCL: Protein-Ligand CONSTRAINED Docking Message-Id: <-37324-080711005948-12951-NTUNpc5PjXoJlHlL7cdmaA!^!server.ccl.net> X-Original-From: Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Fri, 11 Jul 2008 14:23:51 +1000 MIME-Version: 1.0 Sent to CCL by: [Vidana.Epa^csiro.au] Hi Richard, Doesn't the "-fmatch" option of Surflex-Dock (constraining the docking to a pre-placed fragment) do what you need to achieve? I am also curious as to why you came to the conclusion that Glide is not up to your standards. Cheers, Vidana. Vidana C. Epa =20 CSIRO, Division of Molecular Health & Technologies, 343 Royal Parade, Parkville, Victoria 3052, AUSTRALIA. =20 tel: (61) - 3 - 9662 - 7345 fax:(61) - 3 - 9662 - 7347 =20 email: Vidana.Epa++csiro.au -----Original Message----- > From: owner-chemistry++ccl.net [mailto:owner-chemistry++ccl.net]=20 Sent: Friday, 11 July 2008 8:07 AM To: Epa, Vidana (CMHT, Parkville) Subject: CCL: Protein-Ligand CONSTRAINED Docking Sent to CCL by: "Richard Wood" [rwoodphd##msn.com] Hi all, I have a series of ligands which I've docked to a protein using=20 Surflex-Dock as implemented in Sybyl. Unfortunately, my results don't explain some experimental observations=20 so I would like to do some contrained docking. I've been looking into FlexX-Pharm, but it seems to only allow one to constrain an ELEMENT of the ligand to be a certain radius from a certain atom (which one can choose) in the protein target. For example, one can pick a nitrogen in a ligand to be within a 3.0 Angstrom radius of a given protein atom, say. This is problematic if your ligand has several nitrogens or carbons in=20 them, as one cannot pick atom types or atom numbers. I'm wondering if=20 there is a workaround to this; I'd like to stay with Sybyl as my boss=20 wants me to use it, and we've decided Glide is not up to our standards.=20 To conclude, I would like to be able to pick a particular ligand atom and constrain it to be a certain distance from a protein atom, that I again pick, and then dock it. As it stands now, I can only constrain a (any) nitrogen in my ligand (I think the fact that my ligand is not introduced at any point, prior to docking, into this process is what is problematic) to be within a radius of a protein atom, and not a fixed distance. Basically, I want to constrain an imidazole nitrogen (say) to be 2.4 Angstroms away from an iron atom in a heme group, or a methyl group to be 3.0 Angstroms from the same atom, and not WITHIN a radius of this distance, since it can be anywhere from 0 to the distance I want, and lead to situations I'm seeing now, where the molecule I'm docking is on top of the heme. TIA, Richard -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt