Article ID: 920 - Last Modified: May 25, 2011
I want to examine the binding of negatively charged sugar chains containing 12-20 sugars (such as heparin) to a target. Can I use Glide to dock these compounds?
Although Glide can be used to dock sugars, you won't be able to use Glide for these compounds, because they are too big for Glide's atom (300) and rotatable bond (50) limits. You could try docking fragments of the molecules.
If docking fragments would not work for you, you could explore other, more computationally intensive, tools, such as dynamics (Desmond, MacroModel, Impact) or conformational searches (MacroModel).
Keywords: sugars, docking, Glide
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