Molecular Docking Server

Covalent docking
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Author:  hayek27 [ Mon Jan 25, 2010 5:17 pm ]
Post subject:  Covalent docking

I would like to 'dock' a ligand that is covalently attached to a Ser active site residue (OG atom). Is it possible to do this using dockingserver? Thanks.

Author:  bikadi [ Mon Jan 25, 2010 6:20 pm ]
Post subject:  Re: Covalent docking

In general, docking methods will never results in forming covalently bound complexes. However, it is still reasonable to try docking in these situations, because the atoms forming the covalent bond should form attractive interactions anyway. The docking result can reflect the real situation, except the bond length of this interaction. If there is no reasonable docking result, you can also consider to remove one hydrogen atom from the covalently bound ligand position. You can do this in the following way:
1, draw your ligand
2, right-click on the given atom
3, set charge to -1
4, in the setup page uncheck the box before pH
5, dock this ligand

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