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通过结合自动和手动方法实现从小型到大型蛋白质的快速准确共振归属。

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

作者信息

Niklasson Markus, Ahlner Alexandra, Andresen Cecilia, Marsh Joseph A, Lundström Patrik

机构信息

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

MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom.

出版信息

PLoS Comput Biol. 2015 Jan 8;11(1):e1004022. doi: 10.1371/journal.pcbi.1004022. eCollection 2015 Jan.

DOI:10.1371/journal.pcbi.1004022
PMID:25569628
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4288728/
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.

摘要

共振归属过程是大多数蛋白质结构与动力学核磁共振研究的基础。不幸的是，手动进行残基归属既繁琐又耗时，并且可能成为进一步表征的重大瓶颈。此外，虽然已经开发出了自动化方法，但它们的准确性往往有限，尤其是对于较大的蛋白质。在此，我们通过引入软件COMPASS来解决这一问题，该软件通过将自动化共振归属与人工干预相结合，能够以大大加快的速度实现接近手动归属的准确性。此外，通过包含补偿氘代蛋白质中同位素位移效应的选项，COMPASS对于较大蛋白质而言比现有的自动化方法更加准确。COMPASS是一个根据GNU通用公共许可证授权的开源项目，可从http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en下载。提供了适用于Linux、Mac OS X和Microsoft Windows的源代码和二进制文件。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/3d762add40e7/pcbi.1004022.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/6dc51b6bb0b3/pcbi.1004022.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/dae39e590540/pcbi.1004022.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/7f1e227acc06/pcbi.1004022.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/7162e974037e/pcbi.1004022.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/513b233bd988/pcbi.1004022.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/f4a81afe3bf5/pcbi.1004022.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/0c42263eaca2/pcbi.1004022.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/3d762add40e7/pcbi.1004022.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/6dc51b6bb0b3/pcbi.1004022.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/dae39e590540/pcbi.1004022.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/7f1e227acc06/pcbi.1004022.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/7162e974037e/pcbi.1004022.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/513b233bd988/pcbi.1004022.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/f4a81afe3bf5/pcbi.1004022.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/0c42263eaca2/pcbi.1004022.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/870a/4288728/3d762add40e7/pcbi.1004022.g008.jpg

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