scholarly journals Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation

2007 ◽  
Vol 3 ◽  
pp. 757-766
Author(s):  
Masakazu Sekijima ◽  
Jun Doi ◽  
Shinya Honda ◽  
Tamotsu Noguchi ◽  
Shigenori Shimizu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Parallel Molecular Dynamics ◽  
Analysis System

scholarly journals Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms

RSC Advances ◽  
2017 ◽  
Vol 7 (46) ◽  
pp. 28580-28590 ◽  
Author(s):  
Peng Sang ◽  
Xing Du ◽  
Li-Quan Yang ◽  
Zhao-Hui Meng ◽  
Shu-Qun Liu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Cold Adaptation ◽  
Energy Landscape ◽  
Serine Proteinase ◽  
Dynamics Simulation ◽  
Proteinase K ◽  
Free Energy Landscape ◽  
Molecular Motions ◽  
Underlying Mechanisms

The physicochemical bases for enzyme cold-adaptation remain elusive.

Energetics and structural characterization of the “DFG-flip” conformational transition of B-RAF kinase: a SITS molecular dynamics study

2017 ◽  
Vol 19 (2) ◽  
pp. 1257-1267 ◽  
Author(s):  
Qiang Shao ◽  
Zhijian Xu ◽  
Jinan Wang ◽  
Jiye Shi ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Conformational Transition ◽  
Energy Landscape ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Raf Kinase ◽  
Kinase A

A combination of a homology modeling technique and an enhanced sampling molecular dynamics simulation implemented using the SITS method is employed to compute a detailed map of the free-energy landscape and explore the conformational transition pathway of B-RAF kinase.

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile
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