Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model.

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Coarse-grained normal mode analysis in structural biology. (2005, background): “Building on the notion that NMA can be used to identify potential motions induced by binding, a computationally tractable way to generate a set of docking targets has been proposed [35].”
ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions (2017, methodology): “Using the principles of NMA, SREFLEX divides a structure into subdomains that are treated as rigid bodies during the first stages of refinement.”
ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement (2004, background): “One major application of normal modes is the identiﬁcation of potential conformational changes, e.g. of enzymes upon ligand binding (7,12,13).”
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis (2006, methodology): “The striking simplicity of this method has made it quite popular (14,15).”
Functional dynamics of PDZ binding domains: a normal-mode analysis. (2005, background): “Delarue and Sanejouand 2002; Doruker and others 2002; Hinsen 1998; Hinsen and others 1999; Marques”