An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data

doi:10.1186/s13015-016-0079-3

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	An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data
	Lu,Jianbo 1,2; Xu,Guoliang 3; Zhang,Shihua3 ; Lu,Benzhuo3
	2016-06-21
发表期刊	Algorithms for Molecular Biology
ISSN	1748-7188
卷号	11 期号:1
摘要	AbstractBackgroundSuperpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address the missing data crudely by ignoring such atoms from their structures.ResultsIn this paper, we propose an effective method for superpositioning pairwise and multiple structures without sequence alignment. It is a two-stage procedure including data reduction and data registration.ConclusionsNumerical experiments demonstrated that our method is effective and efficient. The code package of protein structure superposition method for addressing the cases with missing data is implemented by MATLAB, and it is freely available from: http://sourceforge.net/projects/pssm123/files/?source=navbar
关键词	Superposition Protein structure alignment Iterative closest point
DOI	10.1186/s13015-016-0079-3
语种	英语
WOS记录号	BMC:10.1186/s13015-016-0079-3
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/279
专题	应用数学研究所计算数学与科学工程计算研究所
通讯作者	Zhang,Shihua; Lu,Benzhuo
作者单位	1.National Research Institute for Family Planning; Human Genetics Resource Center 2.Graduate School of Peking Union Medical College 3.Academy of Mathematics and Systems Science, Chinese Academy of Sciences; National Center for Mathematics and Interdisciplinary Sciences
推荐引用方式 GB/T 7714	Lu,Jianbo,Xu,Guoliang,Zhang,Shihua,et al. An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data[J]. Algorithms for Molecular Biology,2016,11(1).
APA	Lu,Jianbo,Xu,Guoliang,Zhang,Shihua,&Lu,Benzhuo.(2016).An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data.Algorithms for Molecular Biology,11(1).
MLA	Lu,Jianbo,et al."An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data".Algorithms for Molecular Biology 11.1(2016).