| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T142 |
0-4 |
Sentence |
denotes |
2.5. |
| T143 |
6-45 |
Sentence |
denotes |
Mm/PBSA binding free energy calculation |
| T144 |
46-207 |
Sentence |
denotes |
The method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. |
| T145 |
208-399 |
Sentence |
denotes |
The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). |
| T146 |
400-531 |
Sentence |
denotes |
The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. |
| T147 |
532-749 |
Sentence |
denotes |
The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. |
| T148 |
750-986 |
Sentence |
denotes |
The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. |
| T149 |
987-1340 |
Sentence |
denotes |
The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. |
| T150 |
1341-1507 |
Sentence |
denotes |
The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively. |
