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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 user interface for the ‘Assign’ module.The browser to the left displays the result of ‘Analyze’. Below the browser there are options to change which file is viewed and how to scan the lists for specific results. Next to these there are tools for assigning the spin systems according to aforementioned indices. Completed assignments are displayed in the interactive protein sequence to the right. Information regarding chemical shifts of assigned spin systems is displayed below the protein sequence and at the bottom right statistics are displayed. The calculated secondary structure is displayed above the protein sequence and is updated when a new fragment is assigned. The menu bar allows for further operations, including displaying warnings and enabling the ’Manual Assignment mode’.
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pcbi-1004022-g006: The user interface for the ‘Assign’ module.The browser to the left displays the result of ‘Analyze’. Below the browser there are options to change which file is viewed and how to scan the lists for specific results. Next to these there are tools for assigning the spin systems according to aforementioned indices. Completed assignments are displayed in the interactive protein sequence to the right. Information regarding chemical shifts of assigned spin systems is displayed below the protein sequence and at the bottom right statistics are displayed. The calculated secondary structure is displayed above the protein sequence and is updated when a new fragment is assigned. The menu bar allows for further operations, including displaying warnings and enabling the ’Manual Assignment mode’.

Mentions: In the Assign’ module the results from ‘Analyze’ are used to perform backbone assignments. Its interface, Fig. 6, consists of a file browser that displays a selected ‘Analyze’ result file, an interactive protein sequence where the progress is displayed as well as a graphical representation of the calculated secondary structure. Information, such as chemical shifts and original names of assigned peaks, as well as statistics regarding backbone assignment completeness, is displayed below the protein sequence.


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 user interface for the ‘Assign’ module.The browser to the left displays the result of ‘Analyze’. Below the browser there are options to change which file is viewed and how to scan the lists for specific results. Next to these there are tools for assigning the spin systems according to aforementioned indices. Completed assignments are displayed in the interactive protein sequence to the right. Information regarding chemical shifts of assigned spin systems is displayed below the protein sequence and at the bottom right statistics are displayed. The calculated secondary structure is displayed above the protein sequence and is updated when a new fragment is assigned. The menu bar allows for further operations, including displaying warnings and enabling the ’Manual Assignment mode’.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1004022-g006: The user interface for the ‘Assign’ module.The browser to the left displays the result of ‘Analyze’. Below the browser there are options to change which file is viewed and how to scan the lists for specific results. Next to these there are tools for assigning the spin systems according to aforementioned indices. Completed assignments are displayed in the interactive protein sequence to the right. Information regarding chemical shifts of assigned spin systems is displayed below the protein sequence and at the bottom right statistics are displayed. The calculated secondary structure is displayed above the protein sequence and is updated when a new fragment is assigned. The menu bar allows for further operations, including displaying warnings and enabling the ’Manual Assignment mode’.
Mentions: In the Assign’ module the results from ‘Analyze’ are used to perform backbone assignments. Its interface, Fig. 6, consists of a file browser that displays a selected ‘Analyze’ result file, an interactive protein sequence where the progress is displayed as well as a graphical representation of the calculated secondary structure. Information, such as chemical shifts and original names of assigned peaks, as well as statistics regarding backbone assignment completeness, is displayed below the protein sequence.

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