Extension of a local backbone description using a structural alphabet:: A new approach to the sequence-structure relationship
Extension of a local backbone description using a structural alphabet:: A new approach to the sequence-structure relationship
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DOI：
10.1110/ps.0220502
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发表时间：
2002-12-01
期刊：
影响因子：
8
通讯作者：
Etchebest, C
中科院分区：
文献类型：
--
作者：
de Brevern, AG;Valadié, H;Etchebest, C
蛋白质块（PB）包括16个蛋白质片段的结构字母表，每个片段5个Cot长。它们使近似和正确预测局部蛋白质三维（3D）结构成为可能。我们选择了72个最常见的序列的5个PB，我们称之为结构词（SW）。对四种不同蛋白质数据库的分析表明，SW覆盖其中92%的氨基酸，并为残基提供了良好的结构近似（即，序列）9 Calpha长。我们提出了他们中的大多数在一个简单的网络，描述了90%的整体残基，有趣的是，包括超过80%的氨基酸存在于线圈。对网络的分析显示了3D描述的特异性和质量，以及局部折叠和氨基酸分布之间的新型关系。结果表明，这些蛋白质数据库的三维结构可以很容易地描述的网络中包含的子图的组合。最后，贝叶斯概率方法将预测率提高了4%。
Protein Blocks (PBs) comprise a structural alphabet of 16 protein fragments, each 5 Cot long. They make it possible to approximate and correctly predict local protein three-dimensional (3D) structures. We have selected the 72 most frequent sequences of five PBs, which we call Structural Words (SWs). Analysis of four different protein data banks shows that SWs cover 92% of the amino acids in them and provide a good structural approximation for residues (i.e., sequences) 9 Calpha long. We present most of them in a simple network that describes 90% of the overall residues and, interestingly, includes more than 80% of the amino acids present in coils. Analysis of the network shows the specificity and quality of the 3D descriptions as well as a new type of relation between local folds and amino acid distribution. The results show that the 3D structure of these protein data banks can be easily described by a combination of subgraphs included in the network. Finally, a Bayesian probabilistic approach improved the prediction rate by 4%.