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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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Examples of input files of the supported formats for COMPASS usage.(A) The HNCACB peak list file exported from Sparky with the column ‘Data Height’, indicating peak intensity. (B) The protein sequence file contains amino acids in uppercase three letter code separated with whitespace. (C) The secondary structure file must contain exactly one secondary structure element for each amino acid in the protein sequence file. The format is ‘xxxx’ for unknown secondary structure element, ‘helx’ for α-helix structure, ‘strd’ for β-strand structure and ‘loop’ for random coil structure written in lowercase letters and separated with whitespace.
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pcbi-1004022-g003: Examples of input files of the supported formats for COMPASS usage.(A) The HNCACB peak list file exported from Sparky with the column ‘Data Height’, indicating peak intensity. (B) The protein sequence file contains amino acids in uppercase three letter code separated with whitespace. (C) The secondary structure file must contain exactly one secondary structure element for each amino acid in the protein sequence file. The format is ‘xxxx’ for unknown secondary structure element, ‘helx’ for α-helix structure, ‘strd’ for β-strand structure and ‘loop’ for random coil structure written in lowercase letters and separated with whitespace.

Mentions: Optionally, a file describing the protein secondary structure can be supplied to aid assignment. This file is ideally derived from the three-dimensional protein structure but secondary structure may also be predicted based on sequence homology. The format of this file is the secondary structure written as ‘helx’ for alpha helices, ‘strd’ for beta strands, ‘loop’ for random coil and ‘xxxx’ for segments of unknown structure. The words should be typed in lower case letters and be separated with whitespace. Note that ‘Convert’ cannot be used to convert to this format. Examples of input files in COMPASS format are shown in Fig. 3.


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)

Examples of input files of the supported formats for COMPASS usage.(A) The HNCACB peak list file exported from Sparky with the column ‘Data Height’, indicating peak intensity. (B) The protein sequence file contains amino acids in uppercase three letter code separated with whitespace. (C) The secondary structure file must contain exactly one secondary structure element for each amino acid in the protein sequence file. The format is ‘xxxx’ for unknown secondary structure element, ‘helx’ for α-helix structure, ‘strd’ for β-strand structure and ‘loop’ for random coil structure written in lowercase letters and separated with whitespace.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1004022-g003: Examples of input files of the supported formats for COMPASS usage.(A) The HNCACB peak list file exported from Sparky with the column ‘Data Height’, indicating peak intensity. (B) The protein sequence file contains amino acids in uppercase three letter code separated with whitespace. (C) The secondary structure file must contain exactly one secondary structure element for each amino acid in the protein sequence file. The format is ‘xxxx’ for unknown secondary structure element, ‘helx’ for α-helix structure, ‘strd’ for β-strand structure and ‘loop’ for random coil structure written in lowercase letters and separated with whitespace.
Mentions: Optionally, a file describing the protein secondary structure can be supplied to aid assignment. This file is ideally derived from the three-dimensional protein structure but secondary structure may also be predicted based on sequence homology. The format of this file is the secondary structure written as ‘helx’ for alpha helices, ‘strd’ for beta strands, ‘loop’ for random coil and ‘xxxx’ for segments of unknown structure. The words should be typed in lower case letters and be separated with whitespace. Note that ‘Convert’ cannot be used to convert to this format. Examples of input files in COMPASS format are shown in Fig. 3.

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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