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期刊论文 [18]
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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
收藏
  |  
浏览/下载:18/0
  |  
提交时间:2021/05/24
Deciphering molecular mechanism behind conformational change of the Sao Paolo metallo-beta-lactamase 1 by using enhanced sampling
期刊论文
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2019, 页码: 12
作者:
Chen, Jianzhong
;
Wang, Jinan
;
Pang, Laixue
;
Wang, Wei
;
Zhao, Juan
收藏
  |  
浏览/下载:47/0
  |  
提交时间:2020/07/01
Sao paolo metallo-beta-lactamase-1
REMD simulations
normal mode analysis
principal component analysis
drug resistance of antibiotics
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations
期刊论文
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2019, 页码: 6
作者:
Qi, Yifei
;
Lee, Jumin
;
Cheng, Xi
;
Shen, Rong
;
Islam, Shahidul M.
收藏
  |  
浏览/下载:16/0
  |  
提交时间:2020/07/01
MDDS simulation
reMD simulation
spin label
EPR
DEER
CHARMM-GUI
Selective enhanced sampling in dihedral energy facilitates overcoming the dihedral energy increase in protein folding and accelerates the searching for protein native structure
期刊论文
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2019, 卷号: 21, 期号: 20, 页码: 10423-10435
作者:
Shao, Qiang
;
Yang, Lijiang
;
Zhu, Weiliang
收藏
  |  
浏览/下载:12/0
  |  
提交时间:2020/07/01
Exploring molecular mechanism of allosteric inhibitor to relieve drug resistance of multiple mutations in HIV-1 protease by enhanced conformational sampling
期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2018, 卷号: 86, 期号: 12, 页码: 1294-1305
作者:
Chen, Jianzhong
;
Peng, Cheng
;
Wang, Jinan
;
Zhu, Weiliang
收藏
  |  
浏览/下载:59/0
  |  
提交时间:2019/01/08
allosteric inhibitor
HIV-1 protease
MM-GBSA
normal mode analysis
REMD
Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example.
期刊论文
Methods in molecular biology (Clifton, N.J.), 2018, 卷号: 1777
作者:
Qi Ruxi
;
Wei Guanghong
;
Ma Buyong
;
Nussinov Ruth
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  |  
浏览/下载:14/0
  |  
提交时间:2019/12/05
Free energy landscape
GROMACS
Human islet amyloid polypeptide
Molecular dynamics simulations
Protein aggregation
REMD
Replica exchange method
Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method
期刊论文
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2017, 卷号: 72, 页码: 136-147
作者:
Han, Mengzhi
;
Xu, Ji
;
Ren, Ying
收藏
  |  
浏览/下载:31/0
  |  
提交时间:2017/05/02
Intrinsically disordered protein
Well-tempered ensemble
Replica exchange with solute tempering
Free energy surface
Molecular dynamics
Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation
期刊论文
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 卷号: 13, 期号: 3, 页码: 1229-1243
作者:
Shao, Qiang
;
Shi, Jiye
;
Zhu, Weiliang
收藏
  |  
浏览/下载:8/0
  |  
提交时间:2019/01/08
Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions
期刊论文
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2016, 卷号: 18, 期号: 42, 页码: 29170-29182
作者:
Shao, Qiang
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  |  
浏览/下载:13/0
  |  
提交时间:2019/01/08
The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view
期刊论文
SCIENTIFIC REPORTS, 2016, 卷号: 6
作者:
Yu, Yuqi
;
Wang, Jinan
;
Shao, Qiang
;
Shi, Jiye
;
Zhu, Weiliang
收藏
  |  
浏览/下载:14/0
  |  
提交时间:2019/01/08
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