Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence
Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence
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DOI：
10.1093/protein/9.2.133
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发表时间：
1996-02-01
期刊：
影响因子：
--
通讯作者：
Argos, P
中科院分区：
文献类型：
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作者：
Frishman, D;Argos, P
现有的基于氨基酸序列的蛋白质二级结构预测方法通常依赖于滑动窗口内局部残基相互作用的统计和中心残基的二级结构状态。这种单残基和单序列预测方法在三个结构阶段（α -螺旋、β -链和线圈）实际实现的准确率极限接近65%，进一步提高预测质量可能需要利用蛋白质三维结构的各个方面。在这里，我们做了这样的尝试，并提出了一种基于识别单个氨基酸序列中潜在氢键残基的二级结构预测的精确算法。我们方法的独特之处是，我们的方法涉及数据库衍生的残基类型出现在不同类别的β桥上的统计数据，以描绘相互作用的β链。根据氢键对（i,i + 4）中出现的氨基酸，也可以识别出α -螺旋结构。该算法在三个结构阶段的预测准确率为68%，仅依赖于单个蛋白质序列作为输入，如果考虑同源比对序列，该算法有可能提高5-7%。
Existing approaches to protein secondary structure prediction from the amino acid sequence usually rely on the statistics of local residue interactions within a sliding window and the secondary structural state of the central residue. The practically achieved accuracy limit of such single residue and single sequence prediction methods is similar to 65% in three structural stages (alpha-helix, beta-strand and coil), Further improvement in the prediction quality is likely to require exploitation of various aspects of three-dimensional protein architecture, Here we make such an attempt and present an accurate algorithm for secondary structure prediction based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence, The unique feature of our approach involves database-derived statistics on residue type occurrences in different classes of beta-bridges to delineate interacting beta-strands. The alpha-helical structures are also recognized on the basis of amino acid occurrences in hydrogen-bonded pairs (i,i + 4). The algorithm has a prediction accuracy of 68% in three structural stages, relies only on a single protein sequence as input and has the potential to be improved by 5-7% if homologous aligned sequences are also considered.