Conformational change of proteins arising from normal mode calculations.

By F. Tama, Yves-Henri Sanejouand. Protein Engineering, 2001

874 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3b6ea57bb0f0378608965458c5ec50405ced105a

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Impact of protein conformational diversity on AlphaFold predictions (2021, methodology): “We perform the NMA for the apo form of the protein on the basis that normal modes obtained with the apo form of a given protein give a better description of the conformational change than those obtained with the holo form [53] .”
Evolutionary Conserved Positions Define Protein Conformational Diversity (2016, background): “A number of studies applied on vastly different enzymes show that conformational transitions are dominated by only a few low-frequency normal modes[35,46,47].”
ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement (2004, background): “Moreover, when the collective character of the protein motion is obvious, a single lowfrequency normal mode often proves to be enough, and it is usually one of the three lowest-frequency ones (12,13).”
Coarse-grained normal mode analysis in structural biology. (2005, background): “The free energy changes associated with H/D exchange of individual amino acids measured near native state conditions for a series of proteins have been correlated, for example, with the entropic costs predicted by the GNM [54]; the experimentally observed structural changes of enzymes between their ”
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis (2006, background): “The server provides functionality to calculate ‘overlap coefficients’ (scalar products) between the coordinate difference vectors of two superimposed structures and the eigenvectors of the 100 lowest frequency normal modes (23).”
Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. (2002, methodology): “The index of collectiveness of each mode was defined and calculated as described.(47) All programs used here are available upon request (sanejouand@crpp.”
iMod: multipurpose normal mode analysis in internal coordinates (2011, positive): “It is well known that NMA performs better from open forms (Tama and Sanejouand, 2001).”
Principles of Flexible Protein-Protein Docking (2008, background): “It has been shown43,44 that the first few normal modes, with the lowest frequencies, can describe much of a conformational change.”