ITP OpenIR  > SCI期刊论文
Gong, LC; Zhou, X; Ouyang, ZC; Zhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping
Source PublicationPLOS ONE
Language英语
AbstractMolecular dynamics (MD) simulation is an important tool for understanding bio-molecules in microscopic temporal/spatial scales. Besides the demand in improving simulation techniques to approach experimental scales, it becomes more and more crucial to develop robust methodology for precisely and objectively interpreting massive MD simulation data. In our previous work [J Phys Chem B 114, 10266 (2010)], the trajectory mapping (TM) method was presented to analyze simulation trajectories then to construct a kinetic transition network of metastable states. In this work, we further present a top-down implementation of TM to systematically detect complicate features of conformational space. We first look at longer MD trajectory pieces to get a coarse picture of transition network at larger time scale, and then we gradually cut the trajectory pieces in shorter for more details. A robust clustering algorithm is designed to more effectively identify the metastable states and transition events. We applied this TM method to detect the hierarchical structure in the conformational space of alanine-dodeca-peptide from microsecond to nanosecond time scales. The results show a downhill folding process of the peptide through multiple pathways. Even in this simple system, we found that single common-used order parameter is not sufficient either in distinguishing the metastable states or predicting the transition kinetics among these states.
2015
Volume10Issue:5Pages:UNSP e0125932
Subject AreaScience & Technology - Other Topics
DOIhttp://dx.doi.org/10.1371/journal.pone.0125932
Indexed BySCI
Funding OrganizationNational Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; National Science Foundation of China [11175250] ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences ; Hundred of Talents Program in Chinese Academy of Sciences
Citation statistics
Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/21006
CollectionSCI期刊论文
Corresponding AuthorZhou, X (reprint author), Univ Chinese Acad Sci, Sch Phys, Beijing 100049, Peoples R China.
Recommended Citation
GB/T 7714
Gong, LC,Zhou, X,Ouyang, ZC,et al. Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping[J]. PLOS ONE,2015,10(5):UNSP e0125932.
APA Gong, LC,Zhou, X,Ouyang, ZC,&Zhou, X .(2015).Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping.PLOS ONE,10(5),UNSP e0125932.
MLA Gong, LC,et al."Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping".PLOS ONE 10.5(2015):UNSP e0125932.
Files in This Item:
File Name/Size DocType Version Access License
Systematically Const(5127KB)期刊论文出版稿开放获取CC BY-NC-SAApplication Full Text
Related Services
Recommend this item
Bookmark
Usage statistics
Export to Endnote
Google Scholar
Similar articles in Google Scholar
[Gong, LC]'s Articles
[Zhou, X]'s Articles
[Ouyang, ZC]'s Articles
Baidu academic
Similar articles in Baidu academic
[Gong, LC]'s Articles
[Zhou, X]'s Articles
[Ouyang, ZC]'s Articles
Bing Scholar
Similar articles in Bing Scholar
[Gong, LC]'s Articles
[Zhou, X]'s Articles
[Ouyang, ZC]'s Articles
Terms of Use
No data!
Social Bookmark/Share
All comments (0)
No comment.
 

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