Cano, Carolina and Brunner, Konrad and Baskaran, Kumaran and Elsner, Ralph and Munte, Claudia E. and Kalbitzer, Hans Robert (2009) Protein structure calculation with data imputation: the use of substitute restraints. JOURNAL OF BIOMOLECULAR NMR, 45 (4). pp. 397-411. ISSN 0925-2738, 1573-5001
Full text not available from this repository. (Request a copy)Abstract
The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It creates a large set of substitute restraints that are used either alone or together with the experimental restraints. The new approach was successfully tested on three examples: firstly, the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the mutant HPr (H15A) from Staphylococcus aureus, and a X-ray structure of human ubiquitin. In all three examples, the quality of the resulting final bundles was improved considerably by the use of additional substitute restraints, as assessed quantitatively by the calculation of RMSD values to the "true" structure and NMR R-factors directly calculated from the original NOESY spectra or the published diffraction data.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | SPARSE NMR DATA; AUTOMATED NOE ASSIGNMENT; DISTANCE RESTRAINTS; SMALL NUMBER; STRUCTURE REFINEMENT; STRUCTURE PREDICTION; SECONDARY STRUCTURE; COUPLING-CONSTANTS; CHEMICAL-SHIFTS; MISSING DATA; Protein structure determination; Missing values; Substitute restraints; Data imputation |
| Subjects: | 500 Science > 570 Life sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Biophysik und physikalische Biochemie > Prof. Dr. Dr. Hans Robert Kalbitzer |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 31 Aug 2020 08:41 |
| Last Modified: | 31 Aug 2020 08:41 |
| URI: | https://pred.uni-regensburg.de/id/eprint/28052 |
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