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Exploring the structural transition mechanisms of a pair of poly(N-isopropylacrylamide) chains in aqueous solution through coarse-grained molecular simulations coupled with metadynamics
期刊论文
MOLECULAR SIMULATION, 2021, 页码: 10
作者:
Yang, Xue-Dan
;
Chen, Wei
;
Ren, Ying
;
Chu, Liang-Yin
收藏
  |  
浏览/下载:24/0
  |  
提交时间:2021/03/29
Poly(N-isopropylacrylamide)
Coarse-grained molecular dynamics
free energy
metadynamics
Increasing the Sampling Efficiency of Protein Conformational Change by Combining a Modified Replica Exchange Molecular Dynamics and Normal Mode Analysis
期刊论文
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2021, 卷号: 17, 期号: 1, 页码: 13-28
作者:
Peng, Cheng
;
Wang, Jinan
;
Shi, Yulong
;
Xu, Zhijian
;
Zhu, Weiliang
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  |  
浏览/下载:18/0
  |  
提交时间:2021/05/24
SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations
期刊论文
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2020, 卷号: 34, 期号: 5, 页码: 589-600
作者:
Sun, Zhaoxi
;
He, Qiaole
;
Li, Xiao
;
Zhu, Zhengdan
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  |  
浏览/下载:28/0
  |  
提交时间:2020/07/01
Free energy calculation
Binding pose
Binding affinity
Spherical coordinates
SAMPL6
Revealing the Positive Binding Cooperativity Mechanism between the Orthosteric and the Allosteric Antagonists of CCR2 by Metadynamics and Gaussian Accelerated Molecular Dynamics Simulations
期刊论文
ACS CHEMICAL NEUROSCIENCE, 2020, 卷号: 11, 期号: 4, 页码: 628-637
作者:
An, Xiaoli
;
Bai, Qifeng
;
Bing, Zhitong
;
Liu, Hongli
;
Zhang, Qianqian
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  |  
浏览/下载:21/0
  |  
提交时间:2022/01/18
CC chemokine receptor 2
orthosteric antagonist
allosteric antagonist
binding cooperativity
metadynamics simulation
Gaussian accelerated MD simulation
Computational Insight Into the Small Molecule Intervening PD-L1 Dimerization and the Potential Structure-Activity Relationship
期刊论文
FRONTIERS IN CHEMISTRY, 2019, 卷号: 7, 页码: 15
作者:
Shi, Danfeng
;
An, Xiaoli
;
Bai, Qifeng
;
Bing, Zhitong
;
Zhou, Shuangyan
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  |  
浏览/下载:24/0
  |  
提交时间:2022/01/19
PD-L1
small-molecule inhibitors
molecular dynamics simulation
metadynamics simulation
R-group QSAR
Enhanced sampling in molecular dynamics
期刊论文
JOURNAL OF CHEMICAL PHYSICS, 2019, 卷号: 151, 期号: 7, 页码: 9
作者:
Yang, Yi Isaac
;
Shao, Qiang
;
Zhang, Jun
;
Yang, Lijiang
;
Gao, Yi Qin
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  |  
浏览/下载:3/0
  |  
提交时间:2020/07/01
All-atom structure ensembles of islet amyloid polypeptides determined by enhanced sampling and experiment data restraints
期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2019, 卷号: 87, 期号: 7, 页码: 541-550
作者:
Su, Xinyue
;
Wang, Ke
;
Liu, Na
;
Chen, Jiawen
;
Li, Yong
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  |  
浏览/下载:72/0
  |  
提交时间:2019/10/14
aggregation
chemical shift restraint
islet amylod polypeptide
metadynamics
The cloud point phenomenon of ionic surfactants: A view from molecular dynamics and metadynamics simulation
期刊论文
JOURNAL OF MOLECULAR LIQUIDS, 2018, 卷号: 269, 页码: 298-303
作者:
Liu, Guokui
;
Feng, Jin
;
Wang, Honglei
;
Gao, Fengfeng
;
Wei, Yaoyao
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  |  
浏览/下载:42/0
  |  
提交时间:2018/12/21
Molecular dynamics
Metadynamics simulations
Cloud point
Tetrabutylammonium dodecyl sulfate
The cloud point phenomenon of ionic surfactants: A view from molecular dynamics and metadynamics simulation
期刊论文
JOURNAL OF MOLECULAR LIQUIDS, 2018, 卷号: 269, 页码: 298-303
作者:
Liu, Guokui
;
Feng, Jin
;
Wang, Honglei
;
Gao, Fengfeng
;
Wei, Yaoyao
收藏
  |  
浏览/下载:2/0
  |  
提交时间:2019/12/11
Molecular dynamics
Metadynamics simulations
Cloud point
Tetrabutylammonium dodecyl sulfate
Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino AcidsSCI原文链接
期刊论文
2018, 卷号: 19, 期号: 3
作者:
Cao, Zanxia[1,2]
;
Bian, Yunqiang[1]
;
Hu, Guodong[1,2]
;
Zhao, Liling[1,2]
;
Kong, Zhenzhen[1,3]
收藏
  |  
浏览/下载:8/0
  |  
提交时间:2020/01/07
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