Research Article

Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

Figure 5

Typical snapshots for hydrogen bond network between Tamiflu’s charged groups and residues of NA at the binding site obtained by AMBER99SB force field with SPC (a), SPC/E (b), TIP3P (c), and TIP4P (d). Oseltamivir is hydrobonded with –COO and –NH2 (R371, R292); –OH (Y347); − and –COO (D151, E119); NHAc and −NH2 (R152) of NA. All hydrogen atoms are implicit. The lower panel refers to the probability of formation of HBs between ligand and receptor. The results are averaged over the last 2 ns of simulation. Black, red, green, and blue refer to SPC, SPC/E, TIP3P, and TIP4P, respectively.
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