ITP OpenIR  > 理论物理所科研产出  > SCI论文
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.
Incorporating Ab Initio energy into threading approaches for protein structure prediction
Source PublicationBMC BIOINFORMATICS
Language英语
KeywordFold Recognition Alignment Generation Sequences Fragments Profiles
AbstractBackground: 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.
2011
ISSN1471-2105
Volume12Issue:*Pages:S54
Subject AreaPhysics
Indexed BySCI
Citation statistics
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/14407
Collection理论物理所科研产出_SCI论文
Corresponding AuthorZheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China.
Recommended Citation
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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