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Incorporating Ab Initio energy into threading approaches for protein structure prediction
Shao, MF; Wang, S; Wang, C; Yuan, XY; Li, SC; Zheng, WM; Bu, DB; Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China.
2011
发表期刊BMC BIOINFORMATICS
ISSN1471-2105
卷号12期号:*页码:S54
摘要Background: Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches-threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates. Results: In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the "partial" decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function. Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison. Conclusions: Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy.
部门归属[Wang, Sheng; Zheng, Weimou] Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China; [Shao, Mingfu; Wang, Chao; Yuan, Xiongying; Bu, Dongbo] Chinese Acad Sci, Inst Comp Technol, Beijing 100080, Peoples R China; [Li, Shuai Cheng] Int Comp Sci Inst, Berkeley, CA 94704 USA
关键词Fold Recognition Alignment Generation Sequences Fragments Profiles
学科领域Physics
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收录类别SCI
语种英语
WOS记录号WOS:000290221000055
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文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/14407
专题理论物理所SCI论文
通讯作者Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China.
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GB/T 7714
Shao, MF,Wang, S,Wang, C,et al. Incorporating Ab Initio energy into threading approaches for protein structure prediction[J]. BMC BIOINFORMATICS,2011,12(*):S54.
APA Shao, MF.,Wang, S.,Wang, C.,Yuan, XY.,Li, SC.,...&Zheng, WM .(2011).Incorporating Ab Initio energy into threading approaches for protein structure prediction.BMC BIOINFORMATICS,12(*),S54.
MLA Shao, MF,et al."Incorporating Ab Initio energy into threading approaches for protein structure prediction".BMC BIOINFORMATICS 12.*(2011):S54.
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