Introduction

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

Publications

  1. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.
    Cite this
    Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P, 2015-01-01 - PLoS Computational Biology

Credits

  1. Markus Niklasson
    Developer

    Division of Biomolecular Technology, Department of Physics, Sweden

  2. Alexandra Ahlner
    Developer

    Division of Biomolecular Technology, Department of Physics, Sweden

  3. Cecilia Andresen
    Developer

    Division of Biomolecular Technology, Department of Physics, Sweden

  4. Joseph A Marsh
    Developer

    MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, United Kingdom of Great Britain and Northern Ireland

  5. Patrik Lundström
    Investigator

    Division of Biomolecular Technology, Department of Physics, Sweden

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Summary
AccessionBT006575
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionSweden
Submitted ByPatrik Lundström