A combinatorial scoring function for protein-RNA docking
A combinatorial scoring function for protein-RNA docking
复制标题
蛋白质-RNA 对接的组合评分函数
DOI：
10.1002/prot.25253
复制
发表时间：
2017
期刊：
影响因子：
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通讯作者：
Tan Jian Jun
中科院分区：
文献类型：
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作者：
Zhang Zhao;Lu Lin;Zhang Yue;Li Chun Hua;Wang Cun Xin;Zhang Xiao Yi;Tan Jian Jun
蛋白质-RNA对接仍然是一个悬而未决的问题。其中一个主要挑战是开发一个有效的评分函数，可以区分近天然结构和不正确的结构。为了解决这个问题，我们构建了一个基于知识的残基-核苷酸配对势，考虑了非核糖体蛋白质-RNA对接的二级结构信息。在这里，我们开发了一个加权组合评分函数RpveScore，它由成对势和六个基于物理的能量项组成。使用多元线性回归方法通过将评分函数拟合到来自Benchmark II的结合对接诱饵的L_rmsd来优化权重。在35个未结合对接病例上测试评分函数。结果表明，包括所有术语的评分函数RpveScore表现最好。此外，还将RpveScore与基于统计力学的方法导出的势ITScore‐PR以及基于原子的联合统计势QUASI‐RNP和DARS‐RNP进行了比较。前1000个结构的RpveScore成功率为71.6%，近原生结构排在前30位的病例数为35例中的25例。对于32个（91.4%）系统，RpveScore可以找到前5位的结合模式，其蛋白质上的天然界面残基和RNA上的核苷酸不低于50%。此外，还发现长程静电吸引能在区分近天然结构与不正确结构方面起着重要作用。这一工作将有助于蛋白质-RNA对接方法的发展和蛋白质-RNA相互作用的理解。RpveScore程序可在http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85：741-752上向公众提供。© 2016 Wiley Periodicals，Inc.
Protein–RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near‐native structures from the incorrect ones. To solve the problem, we have constructed a knowledge‐based residue‐nucleotide pairwise potential with secondary structure information considered for nonribosomal protein–RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics‐based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics‐based method derived potential ITScore‐PR, and the united atom‐based statistical potentials QUASI‐RNP and DARS‐RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near‐native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long‐range electrostatic attractive energy plays an important role in distinguishing near‐native structures from the incorrect ones. This work can be helpful for the development of protein–RNA docking methods and for the understanding of protein–RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741–752. © 2016 Wiley Periodicals, Inc.