Hi dear
There are many opinion for molecular optimization before docking process, but really its depend on docking software and work type. So my question is that for optimize molecule bond length or ... suggest me a force field or experimental method, like in hyperchem for optimize my molecule for docking.
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Euzébio Guimaraes Barbosa
Use mopac pm6 or pm7. Very rapid and good geometries. Remember to sample cyclic molecules before docking.
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Mohamad Akbari
Hi dear Euzébio
thanks for answer, but i cant understand your mean from "sample cyclic molecules before docking" !
Please let me more information.
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Euzébio Guimaraes Barbosa
Cycles are considered rigid for some docking programs. Hyperchem have tools to deal with it. Dock every possible cycle conformer.
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