Designing succinct structural alphabets

doi:10.1093/bioinformatics/btn165

	Designing succinct structural alphabets
	Li, Shuai Cheng 2; Bu, Dongbo 2,3; Gao, Xin 2; Xu, Jinbo 1; Li, Ming 2
	2008-07-01
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	24 期号:13 页码:I182-I189
摘要	Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the 'structural alphabet' for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments. Results: Integer linear programming technique is applied to derive the best combination of these sequence and structural information items. This approach generates significantly more accurate and succinct structural alphabets with more than 50% improvement over the previous accuracies. With these novel structural alphabets, we are able to construct more accurate protein structures than the state-of-art ab initio protein structure prediction programs such as ROSETTA. We are also able to reduce the Kolodnys library size by a factor of 8, at the same accuracy.
DOI	10.1093/bioinformatics/btn165
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000257169700043
出版者	OXFORD UNIV PRESS
引用统计	被引频次：10[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/2XEOYT63/11237
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Xu, Jinbo
作者单位	1.Toyota Technol Inst, Chicago, IL 60637 USA 2.Univ Waterloo, David R Cheriton Sch Comp Sci, Waterloo, ON N2L 3G1, Canada 3.Chinese Acad Sci, Inst Comp Technol, Beijing 100864, Peoples R China
推荐引用方式 GB/T 7714	Li, Shuai Cheng,Bu, Dongbo,Gao, Xin,et al. Designing succinct structural alphabets[J]. BIOINFORMATICS,2008,24(13):I182-I189.
APA	Li, Shuai Cheng,Bu, Dongbo,Gao, Xin,Xu, Jinbo,&Li, Ming.(2008).Designing succinct structural alphabets.BIOINFORMATICS,24(13),I182-I189.
MLA	Li, Shuai Cheng,et al."Designing succinct structural alphabets".BIOINFORMATICS 24.13(2008):I182-I189.