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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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Schematic description of the four modules of COMPASS.(A) ‘Convert’ transforms provided peak lists and amino acid sequence files into COMPASS format. ‘Label’ assigns peaks to spin systems and labels them. ‘Analyze’ analyzes connectivities among spin systems and calculates the probabilities for all possible assignments for such fragments. ‘Assign’ is the interactive module where the user controls the assignment process, aided by the results from ‘Analyze’. (B) The COMPASS main menu provides easy access to the four modules.
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pcbi-1004022-g001: Schematic description of the four modules of COMPASS.(A) ‘Convert’ transforms provided peak lists and amino acid sequence files into COMPASS format. ‘Label’ assigns peaks to spin systems and labels them. ‘Analyze’ analyzes connectivities among spin systems and calculates the probabilities for all possible assignments for such fragments. ‘Assign’ is the interactive module where the user controls the assignment process, aided by the results from ‘Analyze’. (B) The COMPASS main menu provides easy access to the four modules.

Mentions: The recommended process of using COMPASS, Fig. 1, can be described as follows:


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)

Schematic description of the four modules of COMPASS.(A) ‘Convert’ transforms provided peak lists and amino acid sequence files into COMPASS format. ‘Label’ assigns peaks to spin systems and labels them. ‘Analyze’ analyzes connectivities among spin systems and calculates the probabilities for all possible assignments for such fragments. ‘Assign’ is the interactive module where the user controls the assignment process, aided by the results from ‘Analyze’. (B) The COMPASS main menu provides easy access to the four modules.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1004022-g001: Schematic description of the four modules of COMPASS.(A) ‘Convert’ transforms provided peak lists and amino acid sequence files into COMPASS format. ‘Label’ assigns peaks to spin systems and labels them. ‘Analyze’ analyzes connectivities among spin systems and calculates the probabilities for all possible assignments for such fragments. ‘Assign’ is the interactive module where the user controls the assignment process, aided by the results from ‘Analyze’. (B) The COMPASS main menu provides easy access to the four modules.
Mentions: The recommended process of using COMPASS, Fig. 1, can be described as follows:

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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