Three-dimensional shape-structure comparison method for protein classification
Three-dimensional shape-structure comparison method for protein classification
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DOI：
10.1109/tcbb.2006.43
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发表时间：
2006-07-01
影响因子：
4.5
通讯作者：
Strintzis, Michael Gerassimos
中科院分区：
文献类型：
--
作者：
Daras, Petros;Zarpalas, Dimitrios;Strintzis, Michael Gerassimos
在本文中，三维形状为基础的方法，提出了高效的搜索，检索和分类的蛋白质分子。该方法主要依赖于蛋白质的几何3D结构，该结构由相应的PDB文件产生，其次依赖于它们的一级和二级结构。在对3D结构进行适当定位之后，在平移和缩放方面，对它们应用球面轨迹变换，以便产生基于几何的描述符向量，这些描述符向量是完全旋转不变的，并且完美地描述了它们的3D形状。此外，提取蛋白质分子的一级和二级结构的特征属性，形成基于属性的描述符向量。对描述符向量进行加权并产生综合描述符向量。三种分类方法进行了测试。FSSP/DALI数据库的一部分，它提供了一个结构分类的蛋白质，被用来作为地面真相，以评估所提出的方法的分类精度。实验结果表明，该方法实现了99%以上的分类准确率，同时保持了更简单，更快的DALI方法。
In this paper, a 3D shape-based approach is presented for the efficient search, retrieval, and classification of protein molecules. The method relies primarily on the geometric 3D structure of the proteins, which is produced from the corresponding PDB files and secondarily on their primary and secondary structure. After proper positioning of the 3D structures, in terms of translation and scaling, the Spherical Trace Transform is applied to them so as to produce geometry-based descriptor vectors, which are completely rotation invariant and perfectly describe their 3D shape. Additionally, characteristic attributes of the primary and secondary structure of the protein molecules are extracted, forming attribute-based descriptor vectors. The descriptor vectors are weighted and an integrated descriptor vector is produced. Three classification methods are tested. A part of the FSSP/DALI database, which provides a structural classification of the proteins, is used as the ground truth in order to evaluate the classification accuracy of the proposed method. The experimental results show that the proposed method achieves more than 99 percent classification accuracy while remaining much simpler and faster than the DALI method.