Improved Accuracy in RNA–Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function

2016 ◽  
Vol 12 (9) ◽  
pp. 4688-4697 ◽  
Author(s):  
Junichi Iwakiri ◽  
Michiaki Hamada ◽  
Kiyoshi Asai ◽  
Tomoshi Kameda
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rigid Body ◽  
Force Field ◽  
Scoring Function ◽  
Dynamics Simulation ◽  
Rigid Body Docking ◽  
Improved Accuracy

Molecular Dynamics Simulation of Tri-n-butyl-Phosphate Liquid: A Force Field Comparative Study

2011 ◽  
Vol 116 (1) ◽  
pp. 305-313 ◽  
Author(s):  
Shengting Cui ◽  
Valmor F. de Almeida ◽  
Benjamin P. Hay ◽  
Xianggui Ye ◽  
Bamin Khomami
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Comparative Study ◽  
Force Field ◽  
Dynamics Simulation

GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Soft Matter ◽  
2012 ◽  
Vol 8 (37) ◽  
pp. 9617 ◽  
Author(s):  
Callum J. Dickson ◽  
Lula Rosso ◽  
Robin M. Betz ◽  
Ross C. Walker ◽  
Ian R. Gould
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Dynamics Simulation ◽  
Amber Force Field

New all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve

2007 ◽  
Vol 29 (1) ◽  
pp. 122-129 ◽  
Author(s):  
Matej Praprotnik ◽  
Stanko Hočevar ◽  
Milan Hodošček ◽  
Matej Penca ◽  
Dušanka Janežič
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Force Field ◽  
Molecular Sieve ◽  
Dynamics Simulation
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