Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

Markus Niklasson, Alexandra Ahlner, Cecilia Andresen, Joseph A Marsh, Patrik Lundström

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)e1004022
JournalPLoS Computational Biology
Volume11
Issue number1
DOIs
Publication statusPublished - 8 Jan 2015

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