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题名: Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment
作者: Cao, H; Lu, YG(路永钢)
收录类别: SCIE ; CPCI-S ; MEDLINE
出版日期: 2017-01
会议名称: 8th Computational Structural Bioinformatics Workshop (CSBW)
会议日期: 2015-11-09
会议地点: Washington, DC
英文摘要: With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities. Accordingly, we propose a new flexible protein structure alignment method based on variable-length AFPs. Compared with other methods, the proposed method possesses three main advantages. First, it is based on variable-length AFPs. The length of each AFP is separately determined to maximally represent a local similar structure fragment, which reduces the number of AFPs. Second, it uses local coordinate systems, which simplify the computation at each step of the expansion of AFPs during the AFP identification. Third, it decreases the number of twists by rewarding the situation where nonconsecutive AFPs share the same transformation in the alignment, which is realized by dynamic programming with an improved transition function. The experimental data show that compared with FlexProt, FATCAT, and FlexSnap, the proposed method can achieve comparable results by introducing fewer twists. Meanwhile, it can generate results similar to those of the FATCAT method in much less running time due to the reduced number of AFPs.
关键词: aligned fragment pairs ; dynamic programming ; protein structure alignment
作者部门: [Cao, Hu ; Lu, Yonggang] Lanzhou Univ, Sch Informat Sci & Engn, Lanzhou 730000, Gansu, Peoples R China
通讯作者: Lu, YG (reprint author), Lanzhou Univ, Sch Informat Sci & Engn, Lanzhou 730000, Gansu, Peoples R China.
学科分类: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Computer Science; Mathematical & Computational Biology; Mathematics
所属项目编号: National Science Foundation of China [61272213] ; Fundamental Research Funds for Central Universities [lzujbky-2016-k07]
所属项目名称: 国家自然科学基金项目 ; 中央高校基本科研业务费专项资金
项目资助者: NSFC ; LZU
会议录: JOURNAL OF COMPUTATIONAL BIOLOGY
卷号: 24
期号: 1
页码: 2-12
出版者: MARY ANN LIEBERT, INC
出版地: NEW ROCHELLE
语种: 英语
DOI: 10.1089/cmb.2016.0135
ISSN号: 1066-5277
WOS记录号: WOS:000391761300002
PM记录号: 27710035
IR记录号: WOS:000391761300002
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内容类型: 会议论文
URI标识: http://ir.lzu.edu.cn/handle/262010/189708
Appears in Collections:信息科学与工程学院_会议论文

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Recommended Citation:
Cao, H,Lu, YG. Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment[C]. 见:8th Computational Structural Bioinformatics Workshop (CSBW). Washington, DC. 2015-11-09.
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