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. Author manuscript; available in PMC: 2013 May 8.
Published in final edited form as: J Chem Theory Comput. 2012 Mar 15;8(5):1750–1764. doi: 10.1021/ct200680g

Fig. 5.

Fig. 5

Representative conformations of 2KHO obtained during UNRES/MD simulations, corresponding to (A) type I opening-binding, (B) type II opening binding and (C) binding only. The structure shown in panel A corresponds to a type RI-II run after 66 ns UNRES time, while the structures shown in panels B and C correspond to two separate trajectories from type RI-RII runs after 45 ns and 51 ns UNRES time, respectively. The drawings were done with PyMOL (http://www.pymol.org) and the backbones of the UNRES conformations were converted to all-atom representation by using the knowledge-based algorithm developed by Gront et al.43 to enable to draw the structures in ribbon representation.