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

Benjamin Bardiaux¹ , Aymeric Bernard¹ , Wolfgang Rieping² , Michael Habeck³ , Thérèse E Malliavin¹ and Michael Nilges¹

¹Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, 28, rue du Dr. Roux, 75015 Paris, France

²Dept of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

³Max Planck Institute for Developmental Biology, Spemannstrasse 35 and Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 Tübingen, Germany

author email corresponding author email

BMC Structural Biology 2008, 8:30doi:10.1186/1472-6807-8-30


Published:	5 June 2008

Abstract

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.

Conclusion

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.