Related ArticlesARIAweb: a server for automated NMR structure calculation.
Nucleic Acids Res. 2020 07 02;48(W1):W41-W47
Authors: Allain F, Mareuil F, Ménager H, Nilges M, Bardiaux B
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a method of choice to study the dynamics and determine the atomic structure of macromolecules in solution. The standalone program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and structure calculation is well established in the NMR community. To ultimately provide a perfectly transparent and easy to use service, we designed an online user interface to ARIA with additional functionalities. Data conversion, structure calculation setup and execution, followed by interactive visualization of the generated 3D structures are all integrated in ARIAweb and freely accessible at https://ariaweb.pasteur.fr.
[NMR paper] Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Related Articles Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes.
Front Chem. 2018;6:150
Authors: Jin X, Zhu T, Zhang JZH, He X
Abstract
In this study, the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method was applied for NMR chemical shift calculations of protein-ligand complexes. In the AF-QM/MM approach, the protein binding pocket is automatically divided...
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06-06-2018 01:42 PM
[NMR paper] AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
Related Articles AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.
J Biomol NMR. 2015 Aug 2;
Authors: Swails J, Zhu T, He X, Case DA
Abstract
We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects...
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08-04-2015 03:00 PM
[NMR paper] Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.
Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.
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...
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04-12-2015 04:41 PM
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
PONDEROSA-C/S: clientâ??server based software package for automated protein 3D structure determination
PONDEROSA-C/S: clientâ??server based software package for automated protein 3D structure determination
Abstract
Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727â??1728. doi:10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein...
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09-05-2014 03:03 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...
ARIAweb: a server for automated NMR structure calculation.
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