OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries.
OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries.
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DOI：
10.1016/j.jmb.2008.10.093
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发表时间：
2009-01-30
影响因子：
5.6
通讯作者：
Ma, Jianpeng
中科院分区：
文献类型：
--
作者：
Wu, Yinghao;Dousis, Athanasios D.;Chen, Mingzhi;Li, Jialin;Ma, Jianpeng
在这篇文章中，我们提出了一种从头预测蛋白质结构域边界的方法，称为OPUS-Dom。该方法的核心是一种新的粗粒度折叠方法，VECFOLD，它通过折叠代表预测的二级结构元素的向量链，从靶序列构建低分辨率结构模型。OPUS-Dom通过VECFOLD生成大量的折叠结构诱饵，并通过域解析算法标记每个诱饵的域边界。共识域的边界，然后来自推定的边界和三个经验序列为基础的域配置文件的统计分布。OPUS-Dom通常优于几种最先进的结构域预测算法在各种基准蛋白质集。尽管每个VECFOLD生成的结构都包含很大的错误，但这些结构共同提供了更鲁棒的域边界描绘。OPUS-Dom的成功表明，蛋白质结构域的排列更多的是二级结构片段三级包装产生的每个结构域的有限协调模式的结果，而不是序列特异性约束。
In this article, we present a de novo method for predicting protein domain boundaries, called OPUS-Dom. The core of the method is a novel coarse-grained folding method, VECFOLD, which constructs low-resolution structural models from a target sequence by folding a chain of vectors representing the predicted secondary-structure elements. OPUS-Dom generates a large ensemble of folded structure decoys by VECFOLD and labels the domain boundaries of each decoy by a domain parsing algorithm. Consensus domain boundaries are then derived from the statistical distribution of the putative boundaries and three empirical sequence-based domain profiles. OPUS-Dom generally outperformed several state-of-the-art domain prediction algorithms over various benchmark protein sets. Even though each VECFOLD-generated structure contains large errors, collectively these structures provide a more robust delineation of domain boundaries. The success of OPUS-Dom suggests that the arrangement of protein domains is more a consequence of limited coordination patterns per domain arising from tertiary packing of secondary-structure segments, rather than sequence-specific constraints.
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