Introduction

ARIA (Ambiguous Restraints for Iterative Assignment) is a software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the NOE assignment process through the use of ambiguous distance restraints in an iterative structure calculation scheme. ARIA does not perform itself the structure generation: it drives the structure generation by analyzing the conformers obtained in the previous step to update the restraints and obtain a set of improved conformers. The final step of the calculation is a refinement step by molecular dynamics in explicit solvent. ARIA assess the quality of the final structure, using analyses internal to the program as well as outside tools.

The principles of ARIA are described in the following references:

General principle

M Nilges. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities (1995) J Mol Biol. 245, 645-660. Pubmed

M Nilges, MJ Macias, SI O'Donoghue and H Oschkinat. Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. (1997) J Mol Biol. 269, 408-422. Pubmed

JP Linge, SI O'Donoghue and M Nilges. Automated assignment of ambiguous nuclear Overhauser effects with ARIA (2001) Methods Enzymol. 339, 71-90. Pubmed

The python interface in ARIA

JP Linge, M Habeck, W Rieping and M Nilges M. ARIA: automated NOE assignment and NMR structure calculation (2003) Bioinformatics 19, 315-316. Pubmed


Presentation of the version 2.0 of ARIA

M Habeck, W Rieping, JP Linge and M Nilges. NOE assignment with ARIA 2.0: the nuts and bolts (2004) Methods Mol Biol. 278:379-402. Pubmed


Correction of spin diffusion in upper bounds

JP Linge, M Habeck, W Rieping and M Nilges. Correction of spin diffusion during iterative automated NOE assignment (2004) J Magn Reson. 167, 334-342. Pubmed


Final refinement in explicit solvent

JP Linge, MA Williams, CA Spronk, AM Bonvin and M Nilges. Refinement of protein structures in explicit solvent (2003) Proteins. 50, 496-506. Pubmed


The set of non-bonded parameters used in ARIA

JP Linge and M Nilges. Influence of non-bonded parameters on the quality of NMR structures: a new force field for NMR structure calculation (1999) J Biomol NMR. 13, 51-59. Pubmed


Refinement of multimers

M Nilges. A calculation strategy for the structure determination of symmetric dimers by 1H NMR (1993) Proteins.17, 297-309. Pubmed

SI O'Donoghue, X Chang, R Abseher, M Nilges and JJ Led. Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure (2000) J Biomol NMR. 16, 93-108. Pubmed