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上海药物研究所 [14]
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期刊论文 [35]
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Molecular Mechanism of Binding Selectivity of Inhibitors toward BACE1 and BACE2 Revealed by Multiple Short Molecular Dynamics Simulations and Free-Energy Predictions
期刊论文
ACS CHEMICAL NEUROSCIENCE, 2019, 卷号: 10, 期号: 10, 页码: 4303-4318
作者:
Chen, Jianzhong
;
Wang, Jinan
;
Yin, Baohua
;
Pang, Laixue
;
Wang, Wei
收藏
  |  
浏览/下载:118/0
  |  
提交时间:2020/07/01
beta-amyloid cleaving enzyme
binding selectivity
MSMD
hierarchical clustering analysis
MM-GBSA
Exploring binding mechanisms of VEGFR2 with three drugs lenvatinib, sorafenib, and sunitinib by molecular dynamics simulation and free energy calculation
期刊论文
CHEMICAL BIOLOGY & DRUG DESIGN, 2019, 卷号: 93, 期号: 5, 页码: 934-948
作者:
Wang, Yu
;
Peng, Cheng
;
Wang, Guimin
;
Xu, Zhijian
;
Luo, Yongfeng
收藏
  |  
浏览/下载:20/0
  |  
提交时间:2020/07/01
hydrophobic contact scanning
MM
GBSA
molecular dynamics simulation
VEGFR2-drugs interaction
Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge
期刊论文
FUTURE MEDICINAL CHEMISTRY, 2019, 卷号: 11, 期号: 4, 页码: 303-321
作者:
Peng, Cheng
;
Wang, Jinan
;
Yu, Yuqi
;
Wang, Guimin
;
Chen, Zhaoqiang
收藏
  |  
浏览/下载:5/0
  |  
提交时间:2020/07/01
atomic charge
binding-free energy
electrostatic polarization
semiempirical quantum mechanics
solvated interaction energy
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:61/0
  |  
提交时间:2019/01/08
allosteric inhibitor
HIV-1 protease
MM-GBSA
normal mode analysis
REMD
Inhibiting mechanism of small molecule toward the p53-MDM2 interaction: A molecular dynamic exploration
期刊论文
CHEMICAL BIOLOGY & DRUG DESIGN, 2018, 卷号: 92, 期号: 4, 页码: 1763-1777
作者:
Chen, Jianzhong
;
Wang, Jinan
;
Pang, Laixue
;
Zhu, Weiliang
收藏
  |  
浏览/下载:40/0
  |  
提交时间:2019/01/08
hydrophobic contact scanning
MM-GBSA
p53-MDM2 interaction
principal component analysis
solvated interaction energy
A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation
期刊论文
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2015, 卷号: 33, 期号: 12, 页码: 2606-2618
作者:
Chen, Jianzhong
;
Wang, Jinan
;
Zhang, Qinggang
;
Chen, Kaixian
;
Zhu, Weiliang
收藏
  |  
浏览/下载:18/0
  |  
提交时间:2019/01/08
QM
MM molecular dynamics simulations
MM-GBSA method
trypsin specificity
semi-empirical Hamiltonian
binding free energies
Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation
期刊论文
SCIENTIFIC REPORTS, 2015, 卷号: 5
作者:
Chen, Jianzhong
;
Wang, Jinan
;
Zhang, Qinggang
;
Chen, Kaixian
;
Zhu, Weiliang
收藏
  |  
浏览/下载:20/0
  |  
提交时间:2019/01/08
Allosteric sites can be identified based on the residue-residue interaction energy difference
期刊论文
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2015, 卷号: 83, 期号: 8, 页码: 1375-1384
作者:
Ma, Xiaomin
;
Qi, Yifei
;
Lai, Luhua
收藏
  |  
浏览/下载:27/0
  |  
提交时间:2015/10/27
allosteric site identification
MM
GBSA
energy decomposition
residue-residue interaction energy
CAVITY
Interaction mechanism exploration of R-bicalutamide/S-1 with WT/W741L AR using molecular dynamics simulations
期刊论文
MOLECULAR BIOSYSTEMS, 2015, 卷号: 11, 期号: 12, 页码: 3347-3354
作者:
Liu, HL
;
An, XL
;
Li, SY
;
Wang, YW
;
Li, JZ
收藏
  |  
浏览/下载:4/0
  |  
提交时间:2017/01/11
Allosteric sites can be identified based on the residue-residue interaction energy difference
期刊论文
proteins, 2014
Ma Xiaomin
;
Qi Yifei
;
Lai Luhua
收藏
  |  
浏览/下载:4/0
  |  
提交时间:2015/11/11
CAVITY,MM/GBSA,allosteric site identification,energy decomposition,residue-residue interaction energy
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