ARIA: automated NOE assignment and NMR structure
calculation

Linge, Jens P.; Habeck, Michael; Rieping, Wolfgang; Nilges, Michaël

doi:10.1093/bioinformatics/19.2.315

Cited by 373 publications

(349 citation statements)

References 9 publications

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“…NMR Structure Calculations-The structures were calculated with ARIA (version 1.2) in combination with CNS (28,29). NOE restraints were obtained from three-dimensional 15 N-edited NOESY and threedimensional aliphatic 13 C-edited NOESY spectra.…”

Section: Methodsmentioning

confidence: 99%

Yeast Cox17 Solution Structure and Copper(I) Binding

Abajian

Yatsunyk

Ramirez

et al. 2004

Journal of Biological Chemistry

101

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Section: Methodsmentioning

confidence: 99%

Yeast Cox17 Solution Structure and Copper(I) Binding

Abajian

Yatsunyk

Ramirez

et al. 2004

Journal of Biological Chemistry

101

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“…NMR structure refinement has benefited from advanced semi-automated and automated NOE assignment and structure calculation software like ARIA [4] and CANDID [5,6]. Unlike for crystallographic data, however, the direct analysis of NMR data by computers has been largely limited due to the nature of the data.…”

Section: Introductionmentioning

confidence: 99%

AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic

Masse

Keller

2005

Journal of Magnetic Resonance

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We have developed a new computer algorithm for determining the backbone resonance assignments for biopolymers. The approach we have taken, relative hypothesis prioritization, is implemented as a Lua program interfaced to the recently developed computer-aided resonance assignment (CARA) program. Our program can work with virtually any spectrum type, and is especially good with NOESY data. The results of the program are displayed in an easy-to-read, color-coded, graphic representation, allowing users to assess the quality of the results in minutes. Here we report the application of the program to two RNA recognition motifs of Apobec-1 Complementation Factor. The assignment of these domains demonstrates AutoLinkÕs ability to deliver accurate resonance assignments from very minimal data and with minimal user intervention.

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“…Both calculations were performed with the ISD software; for the Tudor domain, we determined the distance bounds by using the rule implemented in the computer program ARIA. 13 The structures generated with the log-normal model were found to be systematically closer to the X-ray structure than those obtained with the standard procedure ( Table 1). We also observe an improvement in terms of precision.…”

mentioning

confidence: 70%

Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures

2005

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The distribution of the deviation of calculated from measured nuclear Overhauser effect (NOE) intensities is a priori unknown. The use of a log-normal distribution to describe these deviations permits the direct calculation of a structure from the measured intensities without first converting them into distance bounds. We show that the log-normal distribution is a natural choice for describing errors in NOE data and that it improves the accuracy, precision, and quality of the calculated structures compared to the usual bounds representation.

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ARIA: automated NOE assignment and NMR structure calculation

Abstract: XML DTDs (for chemical shifts and NOE crosspeaks), Python scripts for the conversion of various NMR data formats and the results of example calculations using data from the S. cerevisiae HRDC domain are available from: http://www.pasteur.fr/recherche/unites/Binfs/aria/

Cited by 373 publications

References 9 publications

Yeast Cox17 Solution Structure and Copper(I) Binding

Yeast Cox17 Solution Structure and Copper(I) Binding

AutoLink: Automated sequential resonance assignment of biopolymers from NMR data by relative-hypothesis-prioritization-based simulated logic

Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures

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