Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.
Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.
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DOI：
10.1186/1471-2105-9-234
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发表时间：
2008-05-12
影响因子：
3
通讯作者：
Gorin, Andrey A.
中科院分区：
文献类型：
--
作者：
Bordner, Andrew J.;Gorin, Andrey A.
蛋白质之间的相互作用无处不在，对所有细胞过程都是必不可少的。蛋白质复合物的高分辨率x射线晶体结构可以揭示其功能的细节，并为许多计算和实验方法提供基础。区分生物和非生物接触以及完整复合物的重建是一个具有挑战性的计算问题。一个成功的解决方案可以为生物识别的基本原理提供额外的见解，并利用从蛋白质数据库（PDB）中提取的交互信息减少许多算法和数据库中的错误。我们开发了一种鉴定PDB x射线结构中蛋白质复合物的方法，该方法分为四步：(1)全面收集所有蛋白质-蛋白质界面；(2)相似蛋白-蛋白界面聚类；(3)基于一组不同的属性估计每个聚类相关的概率；(4)结合每个PDB条目的这些分数来预测复杂结构。由此产生的生物相关界面簇提供了进化保守蛋白-蛋白相互作用的可靠目录。这些接口，以及预测的蛋白质复合物，可从蛋白质接口服务器（PInS）网站（见可用性和要求部分）获得。我们的方法表明，在从文献中验证的大型基准集上评估的注释错误率几乎降低了两倍。我们还估计了每种界面性质对准确识别生物相关界面的相对贡献，并讨论了进一步改进预测方法的可能方向。
Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes can reveal the details of their function and provide a basis for many computational and experimental approaches. Differentiation between biological and non-biological contacts and reconstruction of the intact complex is a challenging computational problem. A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB). We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) combining these scores for each PDB entry in order to predict the complex structure. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions. These interfaces, as well as the predicted protein complexes, are available from the Protein Interface Server (PInS) website (see Availability and requirements section). Our method demonstrates an almost two-fold reduction of the annotation error rate as evaluated on a large benchmark set of complexes validated from the literature. We also estimate relative contributions of each interface property to the accurate discrimination of biologically relevant interfaces and discuss possible directions for further improving the prediction method.
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