Recognition of base sequence by amino acid side chain : interaction free energy landscape and its dependence on sequence context

2003 ◽  
Vol 43 (supplement) ◽  
pp. S30
Author(s):  
T. Yoshida ◽  
M. Aida ◽  
A. Sarai ◽  
M.Michael Gromiha
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Energy Landscape ◽  
Side Chain ◽  
Free Energy Landscape ◽  
Base Sequence ◽  
Amino Acid Side Chain ◽  
Sequence Context ◽  
Chain Interaction ◽  
Interaction Free Energy

scholarly journals Free-energy landscape of DNA base-amino acid interactions : specificity in the protein-DNA recognition

2000 ◽  
Vol 40 (supplement) ◽  
pp. S92
Author(s):  
M. Aida ◽  
H. Kono ◽  
M.Michael Gromiha ◽  
K. Sayano ◽  
Fabio Pichierri ◽  
...  
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Energy Landscape ◽  
Dna Recognition ◽  
Free Energy Landscape ◽  
Dna Base

Evaluation of free energy landscape for base-amino acid interactions using ab initio force field and extensive sampling

Biopolymers ◽  
2001 ◽  
Vol 61 (1) ◽  
pp. 84-95 ◽  
Author(s):  
T. Yoshida ◽  
T. Nishimura ◽  
M. Aida ◽  
F. Pichierri ◽  
M. M. Gromiha ◽  
...  
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Force Field ◽  
Ab Initio ◽  
Energy Landscape ◽  
Free Energy Landscape

Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations

2010 ◽  
Vol 31 (1) ◽  
pp. 204-216 ◽  
Author(s):  
Alexey K. Shaytan ◽  
Victor A. Ivanov ◽  
Konstantin V. Shaitan ◽  
Alexei R. Khokhlov
Keyword(s):  
Free Energy ◽  
Water Vapor ◽  
Amino Acid ◽  
Md Simulations ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Vapor Interface ◽  
Energy Profiles ◽  
Free Energy Profiles
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