Effect of using suboptimal alignments in template-based protein structure prediction.
Effect of using suboptimal alignments in template-based protein structure prediction.
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DOI：
10.1002/prot.22885
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发表时间：
2011-01
影响因子：
2.9
通讯作者：
Kihara, Daisuke
中科院分区：
文献类型：
--
作者：
Chen, Hao;Kihara, Daisuke
关键词：
计算蛋白质结构预测是蛋白质生物信息学中一个具有挑战性的课题。近年来，由于结构基因组学计划解决的蛋白质结构越来越多，基于模板的结构预测的重要性日益增加。为了充分利用结构基因组学项目所付出的巨大努力和投资，迫切需要建立有效的方法，通过开发利用不能简单地通过同源性识别的远程相关蛋白质的方法来使用已解决的结构作为模板。在这项工作中，我们研究的效果，采用次优的比对基于模板的蛋白质结构预测。我们发现，次优比对往往比最优比对更准确，即使在比对分数很低的情况下，这种准确的次优比对也可能发生。次优比对包含大量正确的氨基酸残基接触。此外，次优比对在用作Modeller的输入时可以改进基于模板的模型。最后，我们采用次优的对齐处理接触电位的概率的方式在线程程序，SUPRB。的概率接触策略优于部分解冻的方法，它只使用最佳的比对在定义残基接触，也重排策略，它使用的接触潜力重排比对。在模板识别测试中与现有方法的比较表明，SUPRB是非常有竞争力的，优于现有的方法。
Computational protein structure prediction remains a challenging task in protein bioinformatics. In the recent years, the importance of template-based structure prediction is increasing due to the growing number of protein structures solved by the structural genomics projects. To capitalize the significant efforts and investments paid on the structural genomics projects, it is urgent to establish effective ways to use the solved structures as templates by developing methods for exploiting remotely related proteins that cannot be simply identified by homology. In this work, we examine the effect of employing suboptimal alignments in template-based protein structure prediction. We showed that suboptimal alignments are often more accurate than the optimal one, and such accurate suboptimal alignments can occur even at a very low rank of the alignment score. Suboptimal alignments contain a significant number of correct amino acid residue contacts. Moreover, suboptimal alignments can improve template-based models when used as input to Modeller. Finally, we employ suboptimal alignments for handling a contact potential in a probabilistic way in a threading program, SUPRB. The probabilistic contacts strategy outperforms the partly thawed approach which only uses the optimal alignment in defining residue contacts and also the reranking strategy, which uses the contact potential in reranking alignments. The comparison with existing methods in the template-recognition test shows that SUPRB is very competitive and outperform existing methods.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
5.6
作者：
GODZIK, A;KOLINSKI, A;SKOLNICK, J
通讯作者：
SKOLNICK, J
影响因子：
8
作者：
Godzik, A
通讯作者：
Godzik, A
影响因子：
2.9
作者：
Jauch, Ralf;Yeo, Hock Chuan;Clarke, Neil D.
通讯作者：
Clarke, Neil D.
影响因子：
2.9
作者：
Chen, Hao;Kihara, Daisuke
通讯作者：
Kihara, Daisuke