title: Determining and visualizing flexibility in protein structures.
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.
authors: Chemistry Department, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.
authors: Walter R P
authors: WR
authors: Scott
authors: Suzana K
authors: SK
authors: Straus
mesh_terms: D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software; D012996:Solutions
chemical_list: D011506:Proteins; D012996:Solutions
keywords: geometric algebra; protein dynamics; protein mobility; protein structure; protein structure comparison