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We investigate several approaches to coarse grained normal mode analysis on protein residual-level structural fluctuations by choosing different ways of representing the residues and the forces among them. Single-atom representations using the backbone atoms C(α), C, N, and C(β) are considered. Combinations of some of these atoms are also tested. The force(More)
The functions of biological structures are related to the dynamics of the structures, especially various kinds of large-amplitude molecular motions. With some assumptions, those motions can be investigated by Normal Mode Analysis (NMA) and Gaussian Network Model (GNM). However, despite their contributions to many applications, the relationship between NMA(More)
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