Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Mathematics, Bioinformatics and Computational Biology

Document Type

Article

Publication Version

Published Version

Publication Date

2008

Journal or Book Title

Journal of Bioinformatics and Computational Biology

Volume

6

Issue

2

First Page

283

Last Page

300

DOI

10.1142/S0219720008003448

Abstract

Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints — NOE, torsion angle, or knowledge-based constraints — or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.

Comments

This article is published as Cui, Feng, Robert Jernigan, and Zhijun Wu. "Knowledge-based versus Experimentally Acquired Distance and Angle Constraints for NMR Structure Refinement." Journal of bioinformatics and computational biology 6, no. 02 (2008): 283-300. doi: 10.1142/S0219720008003448.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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