Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA.
BACKGROUND
The Ambiguous Restraints for Iterative Assignment (ARIA) approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list.


RESULTS
ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i) an interactive contact map, serving as a tool for the analysis of assignments, and (ii) graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level.


CONCLUSIONS
The graphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.
Bardiaux
Benjamin
B
Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, 28, rue du Dr, Roux, 75015 Paris, France. bardiaux@pasteur.fr
Bernard
Aymeric
A
Rieping
Wolfgang
W
Habeck
Michael
M
Malliavin
Thérèse E
TE
Nilges
Michael
M
D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D012984:Software