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J Magn Reson. 2008 Apr;191(2):322-34. doi: 10.1016/j.jmr.2008.01.007. Epub 2008 Jan 16.

REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data.

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1
University of South Carolina, Department of Computer Science and Engineering, 315 Main Street, Columbia, SC 29208, USA.

Abstract

REDCRAFT, a new open source software tool that accommodates the analysis of RDC data for simultaneous structure and dynamics characterization of proteins is presented in this article. Simultaneous consideration of structure and motion is believed to be necessary for accurate representation of the solution-state of a protein. REDCRAFT is designed to primarily utilize RDC data from multiple alignment media in two stages. During Stage-I, a list of possible torsion angles joining any two neighboring peptide planes is ranked based on their fitness to experimental constraints; in Stage-II, a dipeptide fragment is extended by addition of one peptide plane at a time. The algorithm adopted by REDCRAFT is very efficient and can produce a structure for an 80 residue protein within two hours on a typical desktop computer. REDCRAFT exhibits robustness with respect to noise and missing data. REDCRAFT describes the overall alignment of the molecule in the form of an order tensor matrix and is capable of identifying peptide fragments with internal dynamics. Identification of the location of internal motion will permit a more accurate structural representation. Experimental data from two proteins as well as simulated data are presented to illustrate the capabilities of REDCRAFT in both structure determination and identification of the dynamical regions.

PMID:
18258464
PMCID:
PMC2728087
DOI:
10.1016/j.jmr.2008.01.007
[Indexed for MEDLINE]
Free PMC Article
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