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.

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.

Copyright Owner

Inderscience Enterprises Ltd.

Language

en

File Format

application/pdf

Published Version

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