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Resistance mechanism of the oncogenic beta 3-alpha C deletion mutation in BRAF kinase to dabrafenib and vemurafenib revealed by molecular dynamics simulations and binding free energy calculations
期刊论文
CHEMICAL BIOLOGY & DRUG DESIGN, 2019, 卷号: 93, 期号: 2, 页码: 177-187
作者:
Niu, Yuzhen
;
Zhang, Yan
;
Yao, Xiaojun
收藏
  |  
浏览/下载:4/0
  |  
提交时间:2019/12/11
binding free energy calculation
BRAF inhibitors
drug resistance
molecular dynamics simulation
residue interaction network analysis
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:30/0
  |  
提交时间:2015/10/27
allosteric site identification
MM
GBSA
energy decomposition
residue-residue interaction energy
CAVITY
Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598
期刊论文
ANTIVIRAL RESEARCH, 2014, 卷号: 104
-
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  |  
浏览/下载:4/0
  |  
提交时间:2014/12/05
HCV NS5B polymerase
Mutation-induced drug resistance
Molecular docking
MD simulation
Binding free energy calculation
Residue interaction network
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
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  |  
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
Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein
期刊论文
international journal of molecular sciences, 2011
Huang, Yongqi
;
Liu, Zhirong
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  |  
浏览/下载:6/0
  |  
提交时间:2015/11/13
anchor residue
intrinsically disordered proteins
binding promiscuity
molecular recognition features
p53
MDM2
Taz2
MOLECULAR RECOGNITION FEATURES
NATIVELY UNFOLDED PROTEINS
FLY-CASTING MECHANISM
UNSTRUCTURED PROTEINS
CONFORMATIONAL SELECTION
CONSERVED RESIDUES
TRANSACTIVATION DOMAIN
INTERACTION NETWORKS
STRUCTURAL DISORDER
SIDE-CHAINS
Nonnatural protein-protein interaction-pair design by key residues grafting
期刊论文
2010, 2010
Sen Liu
;
Liu, Shiyong
;
Zhu, Xiaolei
;
Liang, Huanhuan
;
Cao, Aoneng
;
Chang, Zhijie
;
Lai, Luhua
收藏
  |  
浏览/下载:3/0
A statistical approach to the prediction of pK(a) values in proteins
期刊论文
2010, 2010, OCT
He, Yun
;
Xu, Jialin
;
Pan, Xian-Ming
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  |  
浏览/下载:2/0
  |  
提交时间:2017/06/15
protein ionizable
residues pKa prediction
residue interaction
protonation
deprotonation
electrostatic
interaction
OVOMUCOID 3RD DOMAIN
CARBOXYL GROUPS
ELECTROSTATIC INTERACTIONS
IONIZATION EQUILIBRIA
DIELECTRIC-CONSTANTS
FREE-ENERGY
CHARGE INTERACTIONS
IONIZABLE RESIDUES
SOLVATED PROTEINS
TITRATABLE GROUPS
Biochemistry & Molecular Biology
Biophysics
Identifying Protein-Protein Interaction Sites Using Granularity Computing of Quotient Space Theory
期刊论文
ROUGH SET AND KNOWLEDGE TECHNOLOGY (RSKT), 2010, 卷号: Vol.6401, 页码: 766-771
作者:
Chen,Xiaoyan
;
Zhang,Yanping
;
Ma,Jun
;
Wang,Yongcheng
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  |  
浏览/下载:2/0
  |  
提交时间:2019/04/24
Protein-protein
interaction
Kernel
covering
algorithms
Granularity
synthesis
Quotient
space
Sequence
profile
Entropy
Residue
accessible
area
Uncover the Conserved Property Underlying Sequence-Distant and Structure-Similar Proteins
期刊论文
BIOPOLYMERS, 2010, 卷号: 93, 期号: 4, 页码: 340-347
作者:
Gao, Jun
;
Li, Zhijun
收藏
  |  
浏览/下载:3/0
  |  
提交时间:2019/12/26
inter-residue interaction
conservation
average number of interactions
homology modeling
Favorable contribution of the C-terminal residue K97 to the stability of a hyperthermophilic archaeal [P62A]Ssh10b
期刊论文
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 2009, 卷号: 481, 期号: 1, 页码: 52-58
Fang, Xianyang
;
Feng, Yingang
;
Wang, Jinfeng
;
王金凤
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  |  
浏览/下载:16/0
  |  
提交时间:2013/12/25
Sulfolobus shibatae
Hyperthermostability
Salt bridge
Electrostatic interaction
C-terminal residue protection
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