Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing.
Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing.
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DOI：
10.1038/s41467-023-37219-z
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发表时间：
2023-03-21
影响因子：
16.6
通讯作者：
Wand, A. Joshua
中科院分区：
文献类型：
--
作者：
Bishop, Anthony C.;Torres-Montalvo, Glorise;Kotaru, Sravya;Mimun, Kyle;Wand, A. Joshua
将核磁共振光谱的共振谱分配给蛋白质中的特定原子仍然是一项劳动密集型和具有挑战性的任务。在利用溶液核磁共振波谱研究蛋白质结构-动力学-功能关系的过程中，指定过程的自动化往往仍然是一个瓶颈。我们提出了一种指认蛋白质主链三共振谱的方法。预测和观察到的化学位移的贝叶斯统计分析与三重共振谱提供的自旋间连接性结合使用，以计算驱动模拟退火法搜索最优共振分配集的伪能势。被称为模拟退火贝叶斯辅助赋值(BARASA)，C++程序实现在大小范围到超过450个氨基酸的系统上进行测试，包括内在无序蛋白质的例子。Barasa速度快、健壮，可容纳不完整和不正确的信息，并且性能优于当前算法--特别是在数据稀疏的情况下，而且速度足够快，可以在数据采集期间进行实时评估。作者提出了一种指定蛋白质主干三重共振谱的方法Barasa，它用观察到的化学位移的贝叶斯统计分析来补充传统的方法。该算法使用模拟退火机来建立一组一致的共振分配，并针对大小不等的系统进行测试，包括超过450个氨基酸，包括内在无序蛋白质的例子。
Assignment of resonances of nuclear magnetic resonance (NMR) spectra to specific atoms within a protein remains a labor-intensive and challenging task. Automation of the assignment process often remains a bottleneck in the exploitation of solution NMR spectroscopy for the study of protein structure-dynamics-function relationships. We present an approach to the assignment of backbone triple resonance spectra of proteins. A Bayesian statistical analysis of predicted and observed chemical shifts is used in conjunction with inter-spin connectivities provided by triple resonance spectroscopy to calculate a pseudo-energy potential that drives a simulated annealing search for the most optimal set of resonance assignments. Termed Bayesian Assisted Assignments by Simulated Annealing (BARASA), a C++ program implementation is tested against systems ranging in size to over 450 amino acids including examples of intrinsically disordered proteins. BARASA is fast, robust, accommodates incomplete and incorrect information, and outperforms current algorithms – especially in cases of sparse data and is sufficiently fast to allow for real-time evaluation during data acquisition. The authors present BARASA, an approach to assign backbone triple resonance spectra of proteins that augments traditional approaches with a Bayesian statistical analysis of the observed chemical shifts. The algorithm employs a simulated annealing engine to establish a consensus set of resonance assignments and is tested against systems ranging in size to over 450 amino acids including examples of intrinsically disordered proteins.
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影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
DOI：
10.1016/j.pnmrs.2013.12.001
发表时间：
2014-04
影响因子：
6.1
作者：
Frueh, Dominique P.
通讯作者：
Frueh, Dominique P.
影响因子：
0.9
作者：
Sapienza PJ;Lee AL
通讯作者：
Lee AL
影响因子：
2.7
作者：
BAX A;IKURA M
通讯作者：
IKURA M
影响因子：
3.7
作者：
Yang Y;Igumenova TI
通讯作者：
Igumenova TI