Campus Units
Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Mathematics
Document Type
Article
Publication Version
Accepted Manuscript
Publication Date
2011
Journal or Book Title
International Journal of Bioinformatics Research and Applications
Volume
7
Issue
2
First Page
146
Last Page
161
DOI
10.1504/IJBRA.2011.040093
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.
Copyright Owner
Inderscience Enterprises Ltd.
Copyright Date
2011
Language
en
File Format
application/pdf
Recommended Citation
Wu, Di; Smith, Stephen; Mahan, Hannah; Jernigan, Robert L.; and Wu, Zhijun, "Analysis of protein dynamics using local-DME calculations" (2011). Biochemistry, Biophysics and Molecular Biology Publications. 149.
https://lib.dr.iastate.edu/bbmb_ag_pubs/149
Included in
Biochemistry Commons, Biophysics Commons, Mathematics Commons, Molecular Biology Commons, Structural Biology Commons
Comments
This is a manuscript of an article published as Wu, Di, Stephen Smith, Hannah Mahan, Robert L. Jernigan, and Zhijun Wu. "Analysis of protein dynamics using local-DME calculations." International journal of bioinformatics research and applications 7, no. 2 (2011): 146-161. doi: 10.1504/IJBRA.2011.040093. Posted with permission.