CCL: Protein-Ligand CONSTRAINED Docking

 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
 CSIRO,
 Division of Molecular Health & Technologies,
 343 Royal Parade,
 Parkville, Victoria 3052,
 AUSTRALIA.
 tel: (61) - 3 - 9662 - 7345
 fax:(61) - 3 - 9662 - 7347
 email: Vidana.Epa++csiro.au
 -----Original Message-----
 > From: owner-chemistry++ccl.net [mailto:owner-chemistry++ccl.net]
 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
 Surflex-Dock as implemented in Sybyl.
 Unfortunately, my results don't explain some experimental observations
 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
 them, as one cannot pick atom types or atom numbers.  I'm wondering if
 there is a workaround to this; I'd like to stay with Sybyl as my boss
 wants me to use it, and we've decided Glide is not up to our standards.
 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
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