| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T94 |
0-82 |
Sentence |
denotes |
Binding Free Energy from Molecular Mechanics Poisson-Boltzmann Surface Area Method |
| T95 |
83-458 |
Sentence |
denotes |
The molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied to calculate the binding energy between RBD and ACE2 in all complexes.47,48 For SARS-COV and nCOV-2019, 200 snapshots of the last 400 ns and for the mutant systems and 100 snapshots of the last 200 ns simulation were used for the calculation of binding free energies with an interval of 2 ns. |
| T96 |
459-656 |
Sentence |
denotes |
Simulation for a few mutant systems (Y449A, T478I, Y489A, and S494P) was extended to 400 ns, and the binding energies were calculated for the last 400 ns to assess the convergence of free energies. |
| T97 |
657-740 |
Sentence |
denotes |
The binding free energy of a ligand–receptor complex can be calculated as:1 2 3 4 5 |
| T98 |
741-948 |
Sentence |
denotes |
In these equations, ΔEMM, ΔGbind, solv, and −TΔS are calculated in the gas phase. ΔEMM is the gas phase molecular mechanical energy changes which includes covalent, electrostatic, and van der Waals energies. |
| T99 |
949-1153 |
Sentence |
denotes |
Based on previous studies, the entropy change during binding is small and neglected in these calculations.48−50 ΔGbind, solv is the solvation free energy which comprises the polar and nonpolar components. |
| T100 |
1154-1287 |
Sentence |
denotes |
The polar solvation is calculated using the MMPBSA method by setting a value of 80 and 2 for solvent and solute dielectric constants. |
| T101 |
1288-1409 |
Sentence |
denotes |
The nonpolar free energy is simply estimated from the solvent accessible surface area (SASA) of the solute from the eq 5. |
