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Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P - PLoS Comput. Biol. (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

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.

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The COMPASS file conversion interface.The file converter enables conversion of peak lists and protein sequence files to formats compatible with COMPASS. The GUI instantly displays which format the protein sequence and peak assignments will be changed to or from.
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pcbi-1004022-g002: The COMPASS file conversion interface.The file converter enables conversion of peak lists and protein sequence files to formats compatible with COMPASS. The GUI instantly displays which format the protein sequence and peak assignments will be changed to or from.

Mentions: To ensure that COMPASS is capable of performing analysis of submitted data it includes a file conversion module. Its interface is shown in Fig. 2. The user can submit the protein sequence and peak lists and convert the data from custom format to COMPASS format. The same module can be used to convert COMPASS output files back to custom format.


Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P - PLoS Comput. Biol. (2015)

The COMPASS file conversion interface.The file converter enables conversion of peak lists and protein sequence files to formats compatible with COMPASS. The GUI instantly displays which format the protein sequence and peak assignments will be changed to or from.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4288728&req=5

pcbi-1004022-g002: The COMPASS file conversion interface.The file converter enables conversion of peak lists and protein sequence files to formats compatible with COMPASS. The GUI instantly displays which format the protein sequence and peak assignments will be changed to or from.
Mentions: To ensure that COMPASS is capable of performing analysis of submitted data it includes a file conversion module. Its interface is shown in Fig. 2. The user can submit the protein sequence and peak lists and convert the data from custom format to COMPASS format. The same module can be used to convert COMPASS output files back to custom format.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Division of Biomolecular Technology, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.

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.

Show MeSH