The conformation of each frame is aligned to a reference structure using the quaternion alignment method [13]. The reference structure is usually selected as one of the conformations in a trajectory. The choice of reference structure is arbitrary, however it is necessary to use the same reference...
Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate
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