We have build 100 units of polymer structure of PVA and PLGA using material studio software for molecular docking studies. The build polymers are very linear and we are unable to dock with our organic molecule. Hence, we need help for reducing the linearity for docking. Please suggest the way/methods for reducing the linearity of the above polymer.
If anybody having build structure for the above polymer, please help us.
Well it's not that easy IMHO. Do you have any experience with the behavior of that polymer?
If the polymer is able to fold into a distinct 3D structure, you would need to perform e.g. a replica exchange MD to get a reasonable structure to dock against. But 100 resiudes are somewhat large, Otherwise you could at least relax it with straight MD for at least 100-200ns for now and see what it is actually behaving like, before making further decisions.
Generally I'd recommend going the same way as it would be a protein, which is also a polymer and methods and workflows are best developed.
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