Harmonicity in slow protein dynamics

By Konrad Hinsen, A. Petrescu, S. Dellerue, M. Bellissent-Funel, G. Kneller. 2000

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The Bio3D packages for structural bioinformatics (2020, methodology): “By default, it implements the efficient C-alpha based model 11 that enables rapid calculation of modes even for large structural ensembles.”
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. (2005, background): “In a theoretical study of neutron scattering spectra (Hinsen et al., 2000), the large-amplitude motions of a protein were described by Brownian motion in an effective harmonic potential.”
Dynamics of proteins in solution (2019, methodology): “…data of large-scale protein motions is a normal mode analysis aiming at the low-frequency Brownian modes (Hinsen, 1998; Doruker et al., 2000; Hinsen et al., 2000; Cui and Bahar, 2006), as implemented in open-source software packages such as the molecular modeling toolkit MMTK (Hinsen, 2000)…”
Integrating protein structural dynamics and evolutionary analysis with Bio3D (2014, methodology): “These include the popular anisotropic network model (ANM) [19], the associated parameter-free ANM [20], and a more sophisticated C-alpha force field derived from fitting to the Amber94 allatom potential [21].”