Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming

doi:10.1016/j.jtbi.2010.10.021

	Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming
	Chen, Ruoying 1,2; Zhang, Zhiwang 3; Wu, Di 4; Zhang, Peng 5; Zhang, Xinyang 1; Wang, Yong 6; Shi, Yong 1,7
	2011-01-21
发表期刊	JOURNAL OF THEORETICAL BIOLOGY
ISSN	0022-5193
卷号	269 期号:1 页码:174-180
摘要	Protein-protein interactions are fundamentally important in many biological processes and it is in pressing need to understand the principles of protein-protein interactions. Mutagenesis studies have found that only a small fraction of surface residues, known as hot spots, are responsible for the physical binding in protein complexes. However, revealing hot spots by mutagenesis experiments are usually time consuming and expensive. In order to complement the experimental efforts, we propose a new computational approach in this paper to predict hot spots. Our method, Rough Set-based Multiple Criteria Linear Programming (RS-MCLP), integrates rough sets theory and multiple criteria linear programming to choose dominant features and computationally predict hot spots. Our approach is benchmarked by a dataset of 904 alanine-mutated residues and the results show that our RS-MCLP method performs better than other methods, e.g., MCLP, Decision Tree, Bayes Net, and the existing HotSprint database. In addition, we reveal several biological insights based on our analysis. We find that four features (the change of accessible surface area, percentage of the change of accessible surface area, size of a residue, and atomic contacts) are critical in predicting hot spots. Furthermore, we find that three residues (Tyr, Trp, and Phe) are abundant in hot spots through analyzing the distribution of amino acids. (C) 2010 Elsevier Ltd. All rights reserved.
关键词	Binding free energy Alanine mutation Residue's features Combined model Predictive performance
DOI	10.1016/j.jtbi.2010.10.021
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[70531040] ; National Natural Science Foundation of China[70921061] ; National Natural Science Foundation of China[70621001] ; Overseas Collaboration Group of Chinese Academy of Sciences ; Chinese Ministry of Science and Technology[2004CB720103] ; BHP Billiton Cooperation of Australia
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
WOS类目	Biology ; Mathematical & Computational Biology
WOS记录号	WOS:000286173000018
出版者	ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
引用统计	被引频次：13[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/12957
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Shi, Yong
作者单位	1.Chinese Acad Sci, Res Ctr Fictitious Econ & Data Sci, Beijing 100190, Peoples R China 2.Chinese Acad Sci, Grad Univ, Coll Life Sci, Beijing 100049, Peoples R China 3.Ludong Univ, Coll Informat Sci & Engn, Yantai 264025, Shandong, Peoples R China 4.Tongji Univ, Dept Biomed Engn, Coll Life Sci & Technol, Shanghai 200092, Peoples R China 5.Chinese Acad Sci, Inst Comp Technol, Beijing 100190, Peoples R China 6.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China 7.Univ Nebraska, Coll Informat Sci & Technol, Omaha, NE 68182 USA
推荐引用方式 GB/T 7714	Chen, Ruoying,Zhang, Zhiwang,Wu, Di,et al. Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming[J]. JOURNAL OF THEORETICAL BIOLOGY,2011,269(1):174-180.
APA	Chen, Ruoying.,Zhang, Zhiwang.,Wu, Di.,Zhang, Peng.,Zhang, Xinyang.,...&Shi, Yong.(2011).Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming.JOURNAL OF THEORETICAL BIOLOGY,269(1),174-180.
MLA	Chen, Ruoying,et al."Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming".JOURNAL OF THEORETICAL BIOLOGY 269.1(2011):174-180.