scholarly journals An optimized charge penetration model for use with the AMOEBA force field

2017 ◽  
Vol 19 (1) ◽  
pp. 276-291 ◽  
Author(s):  
Joshua A. Rackers ◽  
Qiantao Wang ◽  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Ligand Binding ◽  
Force Field ◽  
Short Range ◽  
Electrostatic Model ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base ◽  
Range Error ◽  
Amoeba Force Field

Inclusion of charge penetration corrects the short-range error in the electrostatic model of the AMOEBA force field, and improves the accuracy of interactions ranging from nucleic acid base stacking to protein–ligand binding.

Finding and visualizing nucleic acid base stacking

1996 ◽  
Vol 14 (1) ◽  
pp. 6-11 ◽  
Author(s):  
H.A. Gabb ◽  
S.R. Sanghani ◽  
C.H. Robert ◽  
C. Prévost
Keyword(s):  
Nucleic Acid ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base

scholarly journals The Physical Basis of Nucleic Acid Base Stacking in Water

2001 ◽  
Vol 80 (1) ◽  
pp. 140-148 ◽  
Author(s):  
Ray Luo ◽  
Hillary S.R. Gilson ◽  
Michael J. Potter ◽  
Michael K. Gilson
Keyword(s):  
Nucleic Acid ◽  
Physical Basis ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base
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