Liu Bin, Wang Xiaolong, Lin Lei, Dong Qiwen, Wang Xuan
Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, China.
Comput Biol Chem. 2009 Aug;33(4):303-11. doi: 10.1016/j.compbiolchem.2009.07.001. Epub 2009 Jul 9.
Predicting the binding sites between two interacting proteins provides important clues to the function of a protein. In this study, we present a building block of proteins called order profiles to use the evolutionary information of the protein sequence frequency profiles and apply this building block to produce a class of propensities called order profile interface propensities. For comparisons, we revisit the usage of residue interface propensities and binary profile interface propensities for protein binding site prediction. Each kind of propensities combined with sequence profiles and accessible surface areas are inputted into SVM. When tested on four types of complexes (hetero-permanent complexes, hetero-transient complexes, homo-permanent complexes and homo-transient complexes), experimental results show that the order profile interface propensities are better than residue interface propensities and binary profile interface propensities. Therefore, order profile is a suitable profile-level building block of the protein sequences and can be widely used in many tasks of computational biology, such as the sequence alignment, the prediction of domain boundary, the designation of knowledge-based potentials and the protein remote homology detection.
预测两个相互作用蛋白质之间的结合位点可为蛋白质功能提供重要线索。在本研究中，我们提出了一种名为顺序轮廓的蛋白质构建模块，以利用蛋白质序列频率轮廓的进化信息，并应用此构建模块生成一类称为顺序轮廓界面倾向的倾向。为了进行比较，我们重新审视了残基界面倾向和二元轮廓界面倾向在蛋白质结合位点预测中的应用。将每种倾向与序列轮廓和可及表面积相结合，输入到支持向量机中。在对四种类型的复合物（异源永久性复合物、异源瞬时复合物、同源永久性复合物和同源瞬时复合物）进行测试时，实验结果表明顺序轮廓界面倾向优于残基界面倾向和二元轮廓界面倾向。因此，顺序轮廓是蛋白质序列合适的轮廓级构建模块，可广泛应用于计算生物学的许多任务，如序列比对、结构域边界预测、基于知识的势的指定以及蛋白质远程同源性检测。
