Article ID: 926 - Last Modified: December 4, 2010
Can I dock RNA aptamers to a target with Glide?
Small oligopeptides and oligonucleotides can be docked with Glide, but they must have fewer than 300 atoms and 50 rotatable bonds. Docking very flexible molecules is very challenging, due to the enormous configuration space. If your aptamers are small enough, you could dock them flexibly to a fixed target. You can also consider applying torsional constraints to reduce the number of degrees of freedom.
Keywords: Glide, RNA aptamers
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