IMECH-IR  > 非线性力学国家重点实验室
Substitution Matrices of Residue Triplets Derived from Protein Blocks.
Liu X(刘鑫); Zhao YP(赵亚溥)
Source PublicationJournal of Computational Biology
2010
Volume17Issue:12Pages:1679
ISSN1066-5277
AbstractIn protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.
Keywordhydrophobicity Sequence Alignment Twilight Zone.
Subject Area交叉与边缘领域的力学
DOI10.1089/cmb.2008.0035
Indexed BySCI
Language英语
WOS IDWOS:000285184700005
Citation statistics
Document Type期刊论文
Identifierhttp://dspace.imech.ac.cn/handle/311007/43254
Collection非线性力学国家重点实验室
Corresponding AuthorZhao YP(赵亚溥)
Recommended Citation
GB/T 7714
Liu X,Zhao YP. Substitution Matrices of Residue Triplets Derived from Protein Blocks.[J]. Journal of Computational Biology,2010,17(12):1679.
APA 刘鑫,&赵亚溥.(2010).Substitution Matrices of Residue Triplets Derived from Protein Blocks..Journal of Computational Biology,17(12),1679.
MLA 刘鑫,et al."Substitution Matrices of Residue Triplets Derived from Protein Blocks.".Journal of Computational Biology 17.12(2010):1679.
Files in This Item: Download All
File Name/Size DocType Version Access License
cmb.2008.pdf(362KB) 开放获取LicenseView Download
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[刘鑫]'s Articles
[赵亚溥]'s Articles
Baidu academic
Similar articles in Baidu academic
[刘鑫]'s Articles
[赵亚溥]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[刘鑫]'s Articles
[赵亚溥]'s Articles
Terms of Use
No data!
Social Bookmark/Share
File name: cmb.2008.pdf
Format: Adobe PDF
This file does not support browsing at this time
All comments (0)
No comment.
 

Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.