Systematic probing of an atomic charge set of sialic acid disaccharides for the rational molecular modeling of avian influenza virus based on molecular dynamics simulations.
A systematic searching approach for an atomic charge set through molecular dynamics simulations is introduced to calculate a reasonable sialic acid carbohydrate conformation with respect to the experimentally observed structures. The present molecular dynamics simulation study demonstrated that B3LYP/6-31G is the most suitable basis set for the sialic acid disaccharides, attaining good agreement with experimental data.
Choi
Youngjin
Y
Biochip Research Center, Hoseo University, Asan, Republic of Korea.
Kim
Hyunmyung
H
Cho
Kum Won
KW
Paik
Seung R
SR
Kim
Hyun-Won
HW
Jeong
Karpjoo
K
Jung
Seunho
S
D000818:Animals; D001717:Birds; D002236:Carbohydrate Conformation; D003198:Computer Simulation; D004187:Disaccharides / Q000737:chemistry*; D009980:Influenza A virus / Q000737:chemistry*; D005585:Influenza in Birds / Q000821:virology*; D008958:Models, Molecular; D019158:N-Acetylneuraminic Acid / Q000737:chemistry*
D004187:Disaccharides; D019158:N-Acetylneuraminic Acid