Incorporating Ab Initio energy into threading approaches for protein structure prediction

doi:10.1186/1471-2105-12-S1-S54

	Incorporating Ab Initio energy into threading approaches for protein structure prediction
	Shao,Mingfu 1; Wang,Sheng 2; Wang,Chao 1; Yuan,Xiongying 1; Li,Shuai Cheng 3; Zheng,Weimou 2; Bu,Dongbo 1
	2011-02-15
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	12 期号:Suppl 1
摘要	AbstractBackgroundNative 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.ResultsIn 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.ConclusionsIncorporating Ab Initio energy functions into threading can greatly improve alignment accuracy.
DOI	10.1186/1471-2105-12-S1-S54
语种	英语
WOS记录号	BMC:10.1186/1471-2105-12-S1-S54
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/4007
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zheng,Weimou; Bu,Dongbo
作者单位	1.Chinese Academy of Sciences; Institute of Computing Technology 2.Chinese Academy of Sciences; Institute of Theoretical Physics 3.International Computer Science Institute
推荐引用方式 GB/T 7714	Shao,Mingfu,Wang,Sheng,Wang,Chao,et al. Incorporating Ab Initio energy into threading approaches for protein structure prediction[J]. BMC Bioinformatics,2011,12(Suppl 1).
APA	Shao,Mingfu.,Wang,Sheng.,Wang,Chao.,Yuan,Xiongying.,Li,Shuai Cheng.,...&Bu,Dongbo.(2011).Incorporating Ab Initio energy into threading approaches for protein structure prediction.BMC Bioinformatics,12(Suppl 1).
MLA	Shao,Mingfu,et al."Incorporating Ab Initio energy into threading approaches for protein structure prediction".BMC Bioinformatics 12.Suppl 1(2011).