Article ID: 32 - Last Modified: April 30, 2012
When performing a docking experiment, can I constrain a ligand atom to be within a specific distance range from a receptor atom?
From Suite 2011, you can specify the maximum and minimum distance in the Positional/NOE Constraints tab of the Ligand Docking panel.
In earlier releases, you can do this by performing two consecutive docking runs with positional constraints. In the first run, the ligand atom should be constrained to be within the maximum distance of the receptor atom (i.e. the high end of the distance range). In the second run, the hits from the first run are re-docked and constrained to be within the minimum distance of the receptor atom (i.e., the low end of the distance range). Thus, any poses that are found in the first job but not the second must have the ligand atom in the desired range. This procedure can be used to apply NMR constraints (or NOE constraints) on atom distances.
Keywords: Glide, docking, NMR constraints, NOE constraints, distance constraints
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