TABLE 1.
Overview of systems and previous computational studies.
| System | PDB ID | No. of | Program | Force field (+ charge assignment) | References | |
|---|---|---|---|---|---|---|
| ligands | ligand | protein | ||||
| JNK1 | 2GMX | 21 | FEP+ | OPLS2.1 | OPLS2.1 | Wang et al. (2015) |
| AMBER-TI | RESP charges/GAFF 1.8 | ff14SB | Song et al. (2019) | |||
| pmx/CGenFF | CGenFF v3.0.1 (v4.1) | CHARMM36m | Gapsys et al. (2020) | |||
| FXa | 2RA0 | 11 | AMBER-TI | AM1-BCC/GAFF | ff12SB | Hu et al. (2016) |
| GAL3 | 5E89 | 8 | pmx/CGenFF | CGenFF v3.0.1 (v4.1) | CHARMM36m | Gapsys et al. (2020) |
| CDK2 | 1H1Q | 14 | FEP+ | OPLS2.1 | OPLS2.1 | Wang et al. (2015) |
| AMBER-TI | RESP charges/GAFF 1.8 | ff14SB | He et al. (2020) | |||
| pmx/CGenFF | CGenFF v3.0.1 (v4.1) | CHARMM36m | Gapsys et al. (2020) | |||
| TYK2 | 4GIH | 15 | FEP+ | OPLS2.1 | OPLS2.1 | Wang et al. (2015) |
| AMBER-TI | RESP charges/GAFF 1.8 | ff14SB | Song et al. (2019) | |||
| pmx/CGenFF | CGenFF v3.0.1 (v4.1) | CHARMM36m | Gapsys et al. (2020) | |||