I have a viral envelope glycoprotein with two residues glycosylated with Mannose (NAG, FUC, BMA).
I want to dock these glycans (Glycosylated sites) with the receptor's Carbohydrate Recognition Domain (CRD). The receptor site contains Ca ions that also participate in bindings.
I used Z-dock, Haddock, Hex, Patchdock but none of them gave me results.
Can anybody help me, or suggest useful a tool/server for such dockings?
Thanks
You can also use Vakser lab freely available online tool of GRAMM X, for protein-2 docking...
you can try ICM-pro http://www.molsoft.com/icm_pro.html or cluspro http://cluspro.bu.edu/login.php
May I ask how big is your glycans? I had very good experiences docking small glycans with AutoDock putting very stiff constraint on sugar rotors/cycles. We also managed to do fragment docking with monosaccharides, bound them and submit the whole system to molecular mechanics optimization. We then checked the confirmations of sugar linkages with specific maps derived from the GLYCAM force field (Anne Imberty's lab @ University of Grenoble, France). Hope this helps.
Antoine Daina!! Only one NAG is present at ASN (67) n i want to dock it with CRD (347, 349, 354, Ca, 365 and 367) residues specifically. Can you help me in this?... Autodock gave me error i think coz of my system. How can i contect you? Thanks
Mourad Mesmoudi !! Is it tool? Server? From where i can access it? unable to find :( :'(
Dear Ismatullah,
as I remember the also Schrodinger Suite (http://www.schrodinger.com) could be used for solving your problem. Maybe QM-Polarized docking should be solution of your problem. You may check these two publications: Organic Biomolecular Chemistry, 2011, 9, 5778 – 5786 and Organic Biomolecular Chemistry, 2011, 9, 7705 – 7712 for the reference. And finally you may send me description of your problem (and initial structures) and I will try to make a complex between glycan and CRD for you.
Crtomir
this is actually a very interesting discussion as i too have been trying to dock a GPI anchor with alkaline phosphatase enzyme but have not been successful with auto dock, hex, haddock or GRAMMX.
Modeling of Interactions between lectins and oligosacharides could be very difficult due to several reasons:
a) the binding site on lectine proteins are usually open without well deffined pockets.
b) you need to be very carefull on oligosacharide conformations, only few force fields may predict conformations
correctly (I recommend GLYCAM http://glycam.ccrc.uga.edu/ccrc/).
c) proper treatment of Cations (Ca in this case) that are complexed between oligosaccharide and protein
... etc
Crtomir Podlipnik !!
Thanks alot.. Just Awesum Suite (Schrodinger Suite ).....
Dear Humaria,
Schrodinger Suit is good and you may try Discovery Studio too. Autodock id tricky but Autodock Vina is best to get the result, as it is freely available.
Dear all,
For sugar of course you have to take into account for specific geometries. In your case, ascertain Ca++ charges and radius. Please have a look at this paper, doi:10.1371/journal.pone.0050722. We used a two step approaches involving blind SWISSDOCK (http://www.swissdock.ch) docking followed by local and constrained AUTODOCK (http://autodock.scripps.edu) runs involving GLYCAM (http://glycam.ccrc.uga.edu/ccrc/). It hasworked great and so we were able to dock decasaccharide on the surface of langerine with much confidence.
All methodologies applied are free for academics.
Hope this help.
Antoine.
Thanks alot to all my dear and respected friends. :)
I have docked my protein by PATCHDOCK, and got excellent results.
Once again really a great thanks to all :)
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