Automated backbone assignment of labeled proteins using the threshold accepting algorithm
Automated backbone assignment of labeled proteins using the threshold accepting algorithm
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DOI：
10.1023/a:1008298226961
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发表时间：
1998-01-01
影响因子：
2.7
通讯作者：
Kessler, H
中科院分区：
文献类型：
--
作者：
Leutner, M;Gschwind, RM;Kessler, H
主链共振序列的序列分配是异核磁共振测定蛋白质结构的第一步。对于较大的蛋白质，基于质子侧链信息的分配策略不再适合在自动化过程中使用。因此，我们的程序PASTA（通过阈值接受的蛋白质分配）旨在部分或完全自动化蛋白质的顺序分配，基于核磁共振主干共振和c - β信息的分析。为了克服自动分配过程中峰值重叠和信号缺失带来的问题，PASTA采用阈值接受组合优化策略，该策略优于模拟退火，具有更快的收敛速度和更好的解。通过从已发表的核磁共振数据中复制几个蛋白质的完整顺序骨架分配，表明了该算法的可靠性。通过减少序列信息和增加化学位移容限来重复分配，表明了算法对错配信号、噪声、频谱重叠和缺失峰的鲁棒性。该程序在实际数据上的性能最终通过自动选择人类非胰腺滑膜磷脂酶A(2)的峰值列表来证明，A是一种具有124个残基的蛋白质。
The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus C-beta information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A(2), a protein with 124 residues.