ThreaDom: extracting protein domain boundary information from multiple threading alignments.
ThreaDom: extracting protein domain boundary information from multiple threading alignments.
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ThraDom：从多线程比对中提取蛋白质域边界信息
DOI：
10.1093/bioinformatics/btt209
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发表时间：
2013-07-01
期刊：
影响因子：
--
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Xue Z;Xu D;Wang Y;Zhang Y
动机：蛋白质结构域是可以独立折叠和进化的亚基。结构域边界位置的确定通常是蛋白质折叠和功能注释的第一步。目前的方法大多是通过基于序列的分析来推断域边界，准确性不高。没有有效的方法来预测由来自分离的序列区域的片段组成的不连续结构域。由于基于模板的方法对于蛋白质3D结构建模是最有效的，因此组合多个线程比对信息应该增加计算域预测的准确性和可靠性。结果：我们开发了一种新的蛋白质结构域预测器ThreaDom，它基于多线程比对推断结构域边界位置。该方法开发的核心是结合来自模板结构域结构以及末端和内部比对缺口的信息的结构域保守性得分的推导。在630个非冗余序列上进行测试，不使用同源模板，ThreaDom在81%的情况下生成正确的单域和多域分类，其中78%的情况下具有±20个残基内分配的域接头。在对486个具有不连续结构域的蛋白质进行的第二次测试中，ThreaDom在结构域边界预测中实现了84%的平均准确率和65%的召回率。最后，在来自CASP8的56个靶标上检查了ThreaDom，并且分别与自由建模、硬多结构域和不连续结构域蛋白的靶标具有73%、87%和85%的结构域重叠率，这显著高于CASP8中的大多数结构域预测因子。在最近的CASP9和CASP10实验的靶上获得了类似的结果。可用性：http://zhanglab.ccmb.med.umich.edu/ThreaDom/。联系方式：zhng@umich.edu补充信息：补充数据可从生物信息学在线网站获得。
Motivation: Protein domains are subunits that can fold and evolve independently. Identification of domain boundary locations is often the first step in protein folding and function annotations. Most of the current methods deduce domain boundaries by sequence-based analysis, which has low accuracy. There is no efficient method for predicting discontinuous domains that consist of segments from separated sequence regions. As template-based methods are most efficient for protein 3D structure modeling, combining multiple threading alignment information should increase the accuracy and reliability of computational domain predictions. Result: We developed a new protein domain predictor, ThreaDom, which deduces domain boundary locations based on multiple threading alignments. The core of the method development is the derivation of a domain conservation score that combines information from template domain structures and terminal and internal alignment gaps. Tested on 630 non-redundant sequences, without using homologous templates, ThreaDom generates correct single- and multi-domain classifications in 81% of cases, where 78% have the domain linker assigned within ±20 residues. In a second test on 486 proteins with discontinuous domains, ThreaDom achieves an average precision 84% and recall 65% in domain boundary prediction. Finally, ThreaDom was examined on 56 targets from CASP8 and had a domain overlap rate 73, 87 and 85% with the target for Free Modeling, Hard multiple-domain and discontinuous domain proteins, respectively, which are significantly higher than most domain predictors in the CASP8. Similar results were achieved on the targets from the most recently CASP9 and CASP10 experiments. Availability: http://zhanglab.ccmb.med.umich.edu/ThreaDom/. Contact: zhng@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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