title: Analysis of protein dynamics using local-DME calculations.
abstract: Flexibility and dynamics of protein structures are reflected in the B-factors and order parameters obtained experimentally with X-ray crystallography and Nuclear Magnetic Resonance (NMR). Methods such as Normal Mode Analysis (NMA) and Elastic Network Models (ENM) can be used to predict the fluctuations of protein structures for either atomic level or coarse-grained structures. Here, we introduce the Local-Distance Matrix Error (DME), an efficient and simple analytic method to study the fluctuations of protein structures, especially for the ensembles of NMR-determined protein structures. Comparisons with the fluctuations obtained by experiments and other by computations show strong correlations.
authors.affiliation: Department of Mathematics, Western Kentucky University, Bowling Green, KY 42101, USA. di.wu@wku.edu
authors.forename: Di
authors.initials: D
authors.lastname: Wu
authors.forename: Stephen
authors.initials: S
authors.lastname: Smith
authors.forename: Hannah
authors.initials: H
authors.lastname: Mahan
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
mesh_terms: D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry
chemical_list: D011506:Proteins