In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen

Table 4

Values of Vina score, calculated GROMACS total-energy, and calculated binding free energies using MMPBSA (kJ/mol) of loop and hairpin region truncated from each aptamer. H02a gives the lowest MMPBSA ∆E binding energy compared to other complexes.

Aptamer	Binding energy
	Vina score (kJ/mol)	GROMACS Total energy (kJ/mol)	MM/PBSA ∆E binding (kJ/mol)
H01a	-27.196	-6.32094 x 10^5	-971.119
H01b	-31.798	-7.73169 x 10^5	-977.181
H02a	-24.686	-7.73238 x 10^5	-1303.080
H02b	-24.686	-7.93305 x 10^5	-974.453
H03a	-22.175	-7.71841 x 10^5	-762.144