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Determining and visualizing flexibility in protein structures
Author(s) -
Scott Walter R. P.,
Straus Suzana K.
Publication year - 2015
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24776
Subject(s) - superposition principle , measure (data warehouse) , flexibility (engineering) , protein structure , visualization , biological system , protein dynamics , matrix (chemical analysis) , computer science , molecular dynamics , algorithm , crystallography , physics , chemistry , computational chemistry , data mining , mathematics , biology , statistics , quantum mechanics , chromatography , nuclear magnetic resonance
Abstract How to compare the structures of an ensemble of protein conformations is a fundamental problem in structural biology. As has been previously observed, the widely used RMSD measure due to Kabsch, in which a rigid‐body superposition minimizing the least‐squares positional deviations is performed, has its drawbacks when comparing and visualizing a set of flexible protein structures. Here, we develop a method, fleximatch, of protein structure comparison that takes flexibility into account. Based on a distance matrix measure of flexibility, a weighted superposition of distance matrices rather than of atomic coordinates is performed. Subsequently, this allows a consistent determination of (a) a superposition of structures for visualization, (b) a partitioning of the protein structure into rigid molecular components (core atoms), and (c) an atomic mobility measure. The method is suitable for highlighting both particularly flexible and rigid parts of a protein from structures derived from NMR, X‐ray diffraction or molecular simulation. Proteins 2015; 83:820–826. © 2015 Wiley Periodicals, Inc.