Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.
J Biomol NMR. 2015 Apr 11;
Authors: Mareuil F, Malliavin TE, Nilges M, Bardiaux B
Abstract
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD-NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD-NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.
PMID: 25861734 [PubMed - as supplied by publisher]
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA
Abstract
In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to...
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04-11-2015 12:04 AM
Combined automated NOE assignment and structure calculation with CYANA
Combined automated NOE assignment and structure calculation with CYANA
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but was so far not described in full detail. In this paper we present a complete description of the CYANA implementation of automated NOESY assignment, which differs extensively from...
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03-24-2015 09:48 AM
Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA
Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment...
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03-21-2015 06:18 PM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
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12-15-2012 09:51 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
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12-01-2012 06:10 PM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
Jakob T. Nielsen, Hamid R. Eghbalnia, Niels Chr. Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise,...
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03-09-2012 09:16 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2011
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 23 May 2011</br>
Jakob T., Nielsen , Hamid R., Eghbalnia , Niels Chr., Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we...
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05-24-2011 10:02 PM
[NMR paper] Automated NMR structure calculation with CYANA.
Automated NMR structure calculation with CYANA.
Related Articles Automated NMR structure calculation with CYANA.
Methods Mol Biol. 2004;278:353-78
Authors: Güntert P
This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA. Given a sufficiently complete list of assigned chemical shifts and one or several lists of cross-peak positions and columns from two-, three-, or four-dimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, the assignment of the NOESY...