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![[Figure 1]](ic5119fig1mag.jpg)
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Figure 1
Different methods and representations for different scales of motion. (a) Local motions require specialized force fields, extensive energy minimization and many iterations of molecular dynamics (MD) simulations to capture the effects of detailed interactions between atoms, including surrounding waters and ions. (b) Global motions can be calculated with coarse-grained (CG) representations such as one node per residue at the Cα atom, which can be used with elastic network models (ENMs) and conformational ensembles for normal mode analysis (NMA) and principal component analysis (PCA). These approaches provide fast, analytical methods for extracting mode vectors via matrix decomposition. The structure illustrated is a GluA3 glutamate receptor N-terminal domain dimer, which we have studied extensively using all of these methods (Krieger et al., 2015  ; Lee et al., 2019). |
![[Figure 1]](ic5119fig1.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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