scholarly journals A free energy analysis of nucleic acid base stacking in aqueous solution

1995 ◽  
Vol 69 (4) ◽  
pp. 1528-1535 ◽  
Author(s):  
R.A. Friedman ◽  
B. Honig
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Nucleic Acid ◽  
Energy Analysis ◽  
Base Stacking ◽  
Acid Base ◽  
Nucleic Acid Base ◽  
Free Energy Analysis

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

Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES)

2014 ◽  
Vol 591 ◽  
pp. 137-141 ◽  
Author(s):  
Hiroyuki Shimada ◽  
Taishi Fukao ◽  
Hirotake Minami ◽  
Masatoshi Ukai ◽  
Kentaro Fujii ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Nucleic Acid ◽  
Structural Changes ◽  
Acid Base ◽  
Edge Structure ◽  
X Ray ◽  
Nucleic Acid Base ◽  
X Ray Absorption

Free energy increments for hydrogen bonds in nucleic acid base pairs

1987 ◽  
Vol 109 (12) ◽  
pp. 3783-3785 ◽  
Author(s):  
Douglas H. Turner ◽  
Naoki Sugimoto ◽  
Ryszard Kierzek ◽  
Scott D. Dreiker
Keyword(s):  
Free Energy ◽  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Acid Base ◽  
Base Pairs ◽  
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

ChemInform Abstract: Free Energy Increments for Hydrogen Bonds in Nucleic Acid Base Pairs.

ChemInform ◽  
1987 ◽  
Vol 18 (41) ◽  
Author(s):  
D. H. TURNER ◽  
N. SUGIMOTO ◽  
R. KIERZEK ◽  
S. D. DREIKER
Keyword(s):  
Free Energy ◽  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Acid Base ◽  
Base Pairs ◽  
Nucleic Acid Base

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.

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