STON: A novel method for protein three-dimensional structure comparison

被引：2

作者：

Eslahchi, Changiz ^{[1
,5
]}

Pezeshk, Hamid ^{[2
,3
]}

Sadeghi, Mehdi ^{[4
]}

Rahimi, Amir Massoud ^{[5
]}

Afkham, Heydar Maboudi ^{[1
]}

Arab, Shahriar ^{[6
]}

机构：

[1] Shahid Beheshti Univ, Dept Math Sci, Tehran 1983963113, Iran

[2] Univ Tehran, Sch Math Stat & Comp Sci, Tehran, Iran

[3] Univ Tehran, Univ Coll Sci, Ctr Excellence Biomath, Tehran, Iran

[4] Natl Inst Genet Engn & Biotechnol, Tehran, Iran

[5] Sch Comp Sci, Inst Res Fundamental Sci IPM, Tehran, Iran

[6] Univ Tehran, Inst Biochem & Biophys, Dept Bioinformat, Tehran, Iran

来源：

COMPUTERS IN BIOLOGY AND MEDICINE | 2009年 / 39卷 / 02期

关键词：

Protein structure comparison; Structure alignment; Greedy algorithm; Rigid body transformation; Dihedral angle; STRUCTURE ALIGNMENT; GLOBULAR-PROTEINS; CLASSIFICATION; ALGORITHM; DATABASE; FAMILIES; DISTANCE; SERVER; SCOP;

D O I：

10.1016/j.compbiomed.2008.12.004

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Protein structure comparison is an important problem in bioinformatics and has many applications. in the study of structural and functional genomics. During the last decades, various heuristic methods have been developed to solve the protein structure comparison problem. Most of the protein structure comparison methods give the alignment based on the minimum RMSD (root mean square deviation) and ignore many significant local alignments that may be important for evolutional or functional studies. We have developed a new algorithm to find aligned residues in two proteins with desired RMSD value. The parameterized distance and rotation in this program enable us to search for strongly or weakly similar aligned fragments in two proteins. (C) 2009 Published by Elsevier Ltd.

引用

页码：166 / 172

页数：7

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