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. Author manuscript; available in PMC: 2013 Aug 30.
Published in final edited form as: J Chem Inf Model. 2012 Jul 6;52(7):1821–1832. doi: 10.1021/ci3000997

Figure 2.

Figure 2

Structural stability of a ligand bound to a receptor during equilibration MD simulations. (A) Representative plots of ligand RMSD changes from an initial docked pose as a function of simulations time for near-native pose (RMSD from native pose, RMSDnat = 0.20 Å) and incorrectly docked pose (RMSDnat = 7.15 Å). These plots were prepared from the simulation results for T-3 cognate-receptor docking models. (B) Average ligand RMSDs from the native conformations during last 100-ps simulations (RMSDMD) for the crystal structures.