Comparison of protein secondary structures based on backbone dihedral angles

被引：8

作者：

Wang, Jun ^{[1
,2
]}

Zheng, Xiaoqi ^{[1
]}

机构：

[1] Dalian Univ Technol, Dept Appl Math, Dalian 116024, Peoples R China

[2] Dalian Univ Technol, Coll Avd Sci & Technol, Dalian 116024, Peoples R China

来源：

JOURNAL OF THEORETICAL BIOLOGY | 2008年 / 250卷 / 02期

基金：

中国国家自然科学基金;

关键词：

similarity tree; protein taxonomy; sequence complexity;

D O I：

10.1016/j.jtbi.2007.10.013

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

In this article, we propose a relatively similar measure to compare protein secondary structures. We first transform a protein secondary structure into a special sequence representation (angle sequence) based on a partition of the backbone phi, psi-space. Then, pairwise sequence distance is evaluated on the basis of a symbolic sequence complexity. To illustrate our approach, we construct the similarity tree of 24 proteins from PDB. (c) 2007 Elsevier Ltd. All rights reserved.

引用

页码：382 / 387

页数：6

共 50 条

[31] Coarse-Grained Simulations of Protein Backbone Dynamics. 1. Local Sterics Define the Dihedral Angles
Wagenmann, Andreas
Geyer, Tihamer
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (11) : 4732 - 4745
[32] Genetic Operators Based on Backbone Constraint Angles for Protein Structure Prediction
Santos, Karina B.
Custodio, Fabio L.
Barbosa, Helio J. C.
Dardenne, Laurent E.
2015 IEEE CONFERENCE ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (CIBCB), 2015, : 263 - 270
[33] COMPARING SHORT PROTEIN SUBSTRUCTURES BY A METHOD BASED ON BACKBONE TORSION ANGLES
KARPEN, ME
DEHASETH, PL
NEET, KE
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1989, 6 (02): : 155 - 167
[34] Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias
Ulmschneider, JP
Jorgensen, WL
JOURNAL OF CHEMICAL PHYSICS, 2003, 118 (09): : 4261 - 4271
[35] Correlation between protein secondary structure, backbone bond angles, and side-chain orientations
Lundgren, Martin
Niemi, Antti J.
PHYSICAL REVIEW E, 2012, 86 (02):
[36] Protein φ and ψ dihedral restraints determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures
Richard D. Beger
Philip H. Bolton
Journal of Biomolecular NMR, 1997, 10 : 129 - 142
[37] Determination of the backbone dihedral angles phi in human ubiquitin from reparametrized empirical Karplus equations
Wang, AC
Bax, A
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (10) : 2483 - 2494
[38] RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
Gao, Yujuan
Wang, Sheng
Deng, Minghua
Xu, Jinbo
BMC BIOINFORMATICS, 2018, 19
[39] RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
Yujuan Gao
Sheng Wang
Minghua Deng
Jinbo Xu
BMC Bioinformatics, 19
[40] Dihedral angle based dimensionality reduction for protein structural comparison
Kandiraju, N
Dua, S
Conrad, SA
ITCC 2005: INTERNATIONAL CONFERENCE ON INFORMATION TECHNOLOGY: CODING AND COMPUTING, VOL 1, 2005, : 14 - 19

← 1 2 3 4 5 →