Extend-NMR: Extending NMR for Functional and Structural Genomics
TopSpin MDD PRODECOMP AUREMOL CCPN ARIA ISD HADDOCK CING Deposition
Partner 3:Institut Pasteur, Paris, France
People involved: Michael Nilges, Benjamin Bardiaux, Thérèse E. Malliavin, Aymeric Bernard, Michael Habeck, Wolfgang Rieping
Website: http://aria.pasteur.fr

ARIA: Ambiguous Restraints for Iterative Assignment

The assignment of nuclear Overhauser enhancement (NOE) peaks is the most time-consuming step in the analysis of nuclear magnetic resonance (NMR) data and structure calculation. Though several programs exist that facilitate a manual analysis of spectra, the NOE assignment is tedious due to the large number of assignment possibilities, peak overlap and potential artifacts in the spectra. Therefore, a widely employed approach to NMR structure determination is to calculate a structural model from the experimental data by using programs for automated assignment.

Our computer program ARIA (Ambiguous Restraints for Iterative Assignment) is a widely used software for automated NOE assignment and NMR structure calculation. It speeds up and automatizes the assignment process through the use of an iterative structure calculation scheme. ARIA uses the concept of ambiguous distance restraints (ADR) to automatically assign NOE cross-peaks. Additionally, a spin-diffusion correction procedure, as well as a refinement in explicit water improve the quality of the calculated structures. Moreover, ARIA supports the calculation of symmetric oligomers and protein/protein or protein/nucleic acids complexes.

A graphical user interface (GUI) simplifies and streamlines the setup of a calculation. The GUI enables one to modify all relevant program parameters, such as the iterative protocol and the simulated annealing schedule, the shape of the restraining potentials. The program also offers the option to retrieve input data directly from a CCPN project. This includes details on the molecular system, experimental data such as chemical shifts, NOEs, or residual dipolar couplings, as well as the results of a calculation, most importantly the assigned spectra and the 3D coordinates of the structures. We have incorporated the CCPN data model into ARIA to enable spectroscopists to use existing NMR computer programs in a very efficient way.

Workflow in ARIA: A GUI simplifies the project setup and provides functionality to analyze the generated assignments. The CCPN data model is used for data import, and export of assigned spectra and calculated structures.

ARIA Features

  • Speed-up NOE assignment and structure calculation processes
  • Handling of highly ambiguous data (Ambiguous Distance Restraints, Network-Anchoring)
  • Support for various experimental restraint type
  • Support for symmetric multimers and complexes
  • Spin-diffusion correction and water refinement
  • Graphical User Interface
  • Highly CCPN integrated
Selecting NOESY peak-lists from a CCPNmr project within ARIA GUI
Set-up of ARIA run within Extend-NMR GUI