Prediction of Protein–Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations: Application to Kinase Systems

2013 ◽  
Vol 9 (10) ◽  
pp. 4660-4671 ◽  
Author(s):  
Hironori Kokubo ◽  
Toshimasa Tanaka ◽  
Yuko Okamoto
Keyword(s):  
Ligand Binding ◽  
Umbrella Sampling ◽  
Replica Exchange

Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations

2014 ◽  
Vol 54 (7) ◽  
pp. 2093-2104 ◽  
Author(s):  
Jan K. Marzinek ◽  
Peter J. Bond ◽  
Guoping Lian ◽  
Yanyan Zhao ◽  
Lujia Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ligand Binding ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Α Helix

scholarly journals Implementation of replica-exchange umbrella sampling in GAMESS

2018 ◽  
Vol 228 ◽  
pp. 152-162 ◽  
Author(s):  
Shingo Ito ◽  
Dmitri G. Fedorov ◽  
Yuko Okamoto ◽  
Stephan Irle
Keyword(s):  
Umbrella Sampling ◽  
Replica Exchange
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