Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

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.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 webcite. The Web site also contains an installation guide, a user manual and example calculations.The calculation of an NMR (Nuclear Magnetic Resonance) structure is most often realised in parallel with the assignment of NOEs (Nuclear Overhauser Effect). This task can be automatically performed in the software ARIA (Ambiguous Restraints for Iterative Assignment) [1,2]. The ARIA program uses the concept of Ambiguous Distance Restraints [3] to convert multiple assignment possibilities for an NOE into a single restraint. An iterative protocol allows to identify unlikely assignments and noise peaks to progressively reduce the ambiguity and clean the dataset.In the first iteration, all assignments that are consistent with the chemical shift assignment are applied to the structure. In each iteration, the current set of restraints is used to generate a structure ensemble. Statistics are performed after each iteration on each possible assignment and on how often each restraint is violated as a whole. The least likely assignment possibilit