Comparison of TIP5P water model and TIP4P water model in cluster nucleation kinetics study through umbrella sampling and free energy perturbation

2006 ◽  
Vol 323 (2-3) ◽  
pp. 579-586 ◽  
Author(s):  
Jianzhong Liu ◽  
Liu Yang ◽  
Douglas J. Doren
Keyword(s):  
Free Energy ◽  
Umbrella Sampling ◽  
Water Model ◽  
Free Energy Perturbation ◽  
Kinetics Study ◽  
Nucleation Kinetics ◽  
Energy Perturbation

Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling

2017 ◽  
Vol 19 (44) ◽  
pp. 30239-30248 ◽  
Author(s):  
Jianzhong Chen ◽  
Jinan Wang ◽  
Weiliang Zhu
Keyword(s):  
Free Energy ◽  
Conformational Changes ◽  
Anaplastic Lymphoma Kinase ◽  
Drug Target ◽  
Umbrella Sampling ◽  
Free Energy Perturbation ◽  
Drug Resistant ◽  
Anaplastic Lymphoma ◽  
Energy Perturbation ◽  
Different Levels

Anaplastic lymphoma kinase (ALK) has been regarded as a promising drug target in the treatment of tumors and the mutation L1196M induces different levels of drug resistance toward the existing inhibitors.

scholarly journals Free energy perturbation calculations on binding and catalysis after mutating threonine 220 in subtilisin

1991 ◽  
Vol 266 (18) ◽  
pp. 11801-11809
Author(s):  
N. Mizushima ◽  
D. Spellmeyer ◽  
S. Hirono ◽  
D. Pearlman ◽  
P. Kollman
Keyword(s):  
Free Energy ◽  
Free Energy Perturbation ◽  
Energy Perturbation

scholarly journals Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

2021 ◽  
Vol 7 (3) ◽  
pp. 467-475 ◽  
Author(s):  
Chun-Hui Zhang ◽  
Elizabeth A. Stone ◽  
Maya Deshmukh ◽  
Joseph A. Ippolito ◽  
Mohammad M. Ghahremanpour ◽  
...  
Keyword(s):  
Free Energy ◽  
Free Energy Perturbation ◽  
Main Protease ◽  
Energy Perturbation
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