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. Author manuscript; available in PMC: 2008 Oct 1.
Published in final edited form as: Biochemistry. 2006 Jan 31;45(4):1173–1182. doi: 10.1021/bi0518085

Figure 3.

Figure 3

Several proteins have been explored with the atom-based ANM (where each heavy atom is taken as a node) to determine a suitable cutoff distance for the high-resolution region in the mixed cg. The normalized density of vibrational normal modes, g(ω), for (a) DHFR and (b) free TIM are shown using atom-based models (rcut = 6 and 9 Å) and a residue-based uniform cg model (rcut = 13 Å). The low-frequency end of the spectrum is similar; therefore, either value of the cutoff distances (6 or 9 Å) may be applicable for the high-resolution region in the mixed cg.