NMRFAM-SDF: a protein structure determination framework.
NMRFAM-SDF: a protein structure determination framework.
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DOI：
10.1007/s10858-015-9933-8
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发表时间：
2015-08
影响因子：
2.7
通讯作者：
Markley JL
中科院分区：
文献类型：
--
作者：
Dashti H;Lee W;Tonelli M;Cornilescu CC;Cornilescu G;Assadi-Porter FM;Westler WM;Eghbalnia HR;Markley JL
自动化NMR结构测定的计算要求性质需要对包括数据收集的时间复杂性、化学位移分配的计算复杂性和适当优化步骤的选择在内的因素进行微妙的平衡。在过去的二十年中，该过程的几个离散步骤的计算和算法方面已经得到解决。虽然没有出现单一的综合解决方案，但验证协议的纳入已被公认为是稳健的自动化方法的必要步骤。在结构复杂性较高的蛋白质中，验证的必要性变得更加明显，其中在每个步骤中产生的潜在较大错误可以在结构计算过程中传播和积累，从而显著降低任何软件框架的功效。本文介绍了一个完整的框架，蛋白质结构的NMR测定-从数据采集到结构确定。目的有两个：在可行的情况下，简化非NMR专家的结构确定过程，同时通过提供一组验证每个步骤的模块来保持灵活性，并能够评估错误传播。该框架称为NMRFAM-SDF（NMRFAM-结构确定框架），其各种组件可从NMRFAM网站（http：//nmrfam.wisc.edu/software.htm）下载。本文的在线版本（doi：10.1007/s10858-015-9933-8）包含补充材料，可供授权用户使用。
The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR—from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm). The online version of this article (doi:10.1007/s10858-015-9933-8) contains supplementary material, which is available to authorized users.