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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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Related in: MedlinePlus

User interface for the ‘Analyze’ module.Input files are imported through separate file browser dialogs. The HNCB(i) and HNCB(i)(i-1) may also include 13Cα chemical shifts. The user must select a save directory and a project name. Several additional parameters may be adjusted.
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pcbi-1004022-g005: User interface for the ‘Analyze’ module.Input files are imported through separate file browser dialogs. The HNCB(i) and HNCB(i)(i-1) may also include 13Cα chemical shifts. The user must select a save directory and a project name. Several additional parameters may be adjusted.

Mentions: The purpose of ‘Analyze’ is to analyze spin systems for connectivities, to generate fragments of connected spin systems and to score the fragments for probability of belonging to a certain region of the amino acid sequence. The ‘Analyze’ interface is shown in Fig. 5.


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)

User interface for the ‘Analyze’ module.Input files are imported through separate file browser dialogs. The HNCB(i) and HNCB(i)(i-1) may also include 13Cα chemical shifts. The user must select a save directory and a project name. Several additional parameters may be adjusted.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1004022-g005: User interface for the ‘Analyze’ module.Input files are imported through separate file browser dialogs. The HNCB(i) and HNCB(i)(i-1) may also include 13Cα chemical shifts. The user must select a save directory and a project name. Several additional parameters may be adjusted.
Mentions: The purpose of ‘Analyze’ is to analyze spin systems for connectivities, to generate fragments of connected spin systems and to score the fragments for probability of belonging to a certain region of the amino acid sequence. The ‘Analyze’ interface is shown in Fig. 5.

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
Related in: MedlinePlus