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Article ID: 925 - Last Modified: December 4, 2010

I'm interested in docking small molecules to RNA aptamers. Can I do this with Glide?

Glide treats the receptor structure as rigid and docks the ligands flexibly. If your RNA aptamers are rigid, then you can use Glide for docking. However, if the aptamers are flexible, you should consider other tools such as MacroModel's Embrace conformational search, Prime MM-GBSA, or a dynamics calculation with Desmond.

Keywords: RNA, Glide, docking

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