Refinement of unreliable local regions in template-based protein models
Refinement of unreliable local regions in template-based protein models
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DOI：
10.1002/prot.24086
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发表时间：
2012-08-01
影响因子：
2.9
通讯作者：
Seok, Chaok
中科院分区：
文献类型：
--
作者：
Park, Hahnbeom;Seok, Chaok
当代基于模板的建模技术允许将建模方法应用于大量的生物学问题。然而，即使整体结构可以可靠地建模，它们也往往无法为序列中保守性较低的局部区域提供准确的结构。我们称这些区域为不可靠局部区域（ulr）。ulr的精确建模具有巨大的价值，因为它们经常涉及功能特异性。在本文中，我们通过采用复杂的循环建模技术，介绍了一种在基于模板的模型中建模ulr的新方法。结合我们之前对蛋白质末端的研究，该方法适用于环和末端ulr的细化。在CASP9中进行的盲法大规模测试（蛋白质结构预测技术的第9次关键评估）表明，通过对70%以上成功检测到的ULR进行细化，ULR结构比最初基于模板的模型得到了改进。同样值得注意的是，在12个残基上实现了几个长ulr的成功建模。总的来说，目前的结果表明，在基于模板的建模中，仔细应用循环和终端建模可以成为一种有前途的模型优化工具。2012的蛋白质。(c) 2012 Wiley期刊有限公司
Contemporary template-based modeling techniques allow applications of modeling methods to vast biological problems. However, they tend to fail to provide accurate structures for less-conserved local regions in sequence even when the overall structure can be modeled reliably. We call these regions unreliable local regions (ULRs). Accurate modeling of ULRs is of enormous value because they are frequently involved in functional specificity. In this article, we introduce a new method for modeling ULRs in template-based models by employing a sophisticated loop modeling technique. Combined with our previous study on protein termini, the method is applicable to refinement of both loop and terminus ULRs. A large-scale test carried out in a blind fashion in CASP9 (the 9th Critical Assessment of techniques for protein structure prediction) shows that ULR structures are improved over initial template-based models by refinement in more than 70% of the successfully detected ULRs. It is also notable that successful modeling of several long ULRs over 12 residues is achieved. Overall, the current results show that a careful application of loop and terminus modeling can be a promising tool for model refinement in template-based modeling. Proteins 2012. (c) 2012 Wiley Periodicals, Inc.