ARIA2: Automated NOE assignment and data integration in NMR structure calculation

UNLABELLED Modern structural genomics projects demand for integrated methods for the interpretation and storage of nuclear magnetic resonance (NMR) data. Here we present version 2.1 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation. We report on recent developments, most notably a graphical user interface, and the incorporation of the object-oriented data model of the Collaborative Computing Project for NMR (CCPN). The CCPN data model defines a storage model for NMR data, which greatly facilitates the transfer of data between different NMR software packages. AVAILABILITY A distribution with the source code of ARIA 2.1 is freely available at http://www.pasteur.fr/recherche/unites/Binfs/aria2.

[1]  H Oschkinat,et al.  Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. , 1997, Journal of molecular biology.

[2]  Gert Vriend,et al.  Quantitative evaluation of experimental NMR restraints. , 2003, Journal of the American Chemical Society.

[3]  Thomas Szyperski,et al.  Protein NMR spectroscopy in structural genomics , 2000, Nature Structural Biology.

[4]  Wayne Boucher,et al.  The CCPN data model for NMR spectroscopy: Development of a software pipeline , 2005, Proteins.

[5]  Torsten Herrmann,et al.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. , 2002, Journal of molecular biology.

[6]  V. N. Molchanov,et al.  Superconducting Single Crystals of Tl2Ba2CaCu2O8 and YBa2Cu4O8: Crystal Structures in the Vicinity of Tc , 1998 .

[7]  M Nilges,et al.  Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. , 1995, Journal of molecular biology.

[8]  M. Nilges,et al.  Refinement of protein structures in explicit solvent , 2003, Proteins.

[9]  Miron Livny,et al.  RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank , 2005, Proteins.

[10]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[11]  T. N. Bhat,et al.  A framework for scientific data modeling and automated software development , 2005, Bioinform..