| Protein . | PDB code . | Residue patching . | System’s dimensions (Å × Å × Å) . | Number of atoms . | Duration of the equilibration last step . |
|---|---|---|---|---|---|
| Shakera | A homology model based on 2R9R (Long et al., 2007); see Yazdi et al. (2016) for the details | None | 130 × 130 × 105 | 191,034 | 1 µs |
| NavMs | 5HVX (Sula et al., 2017) | None | 145 × 145 × 120 | 209,838 | 400 ns |
| GLIC | 4NPQ (Sauguet et al., 2014) | None | 110 × 110 × 145 | 159,083 | 1 µs |
| TWIK-1 | 3UKM (Miller and Long, 2012) | Disulfide bond between C78 and C78 (intersubunit) | 105 × 105 × 125 | 127,219 | 200 ns |
| Cx26 | 2ZW3 (Maeda et al., 2009) | Disulfide bonds between C45 and C156, C50 and C152, C56 and C145 | 130 × 130 × 122 | 189,168 | 200 ns |
| VDAC1 | 3EMN (Ujwal et al., 2008) | None | 85 × 85 × 85 | 54,590 | 200 ns |
| TRPV1b | 3J5R (Cao et al., 2013; Liao et al., 2013; Kasimova et al., 2018) | None | 160 × 140 × 175 | 402,346 | 750 ns |
| ClC1 | 6COY (Park and MacKinnon, 2018) | None | 120 × 120 × 100 | 149,529 | 200 ns |
| M2 receptor | 3UON (Haga et al., 2012) | Disulfide bonds between C96 and C176, C413 and C416 | 90 × 90 × 105 | 76,169 | 200 ns |
| Na+/K+ ATPasec | 3WGU (Kanai et al., 2013) | D195, E358, E779, D804, and E954 are protonated; disulfide bonds between C126 and C149, C159 and C175, C213 and C276 | 115 × 115 × 175 | 250,192 | 100 ns |
| Protein . | PDB code . | Residue patching . | System’s dimensions (Å × Å × Å) . | Number of atoms . | Duration of the equilibration last step . |
|---|---|---|---|---|---|
| Shakera | A homology model based on 2R9R (Long et al., 2007); see Yazdi et al. (2016) for the details | None | 130 × 130 × 105 | 191,034 | 1 µs |
| NavMs | 5HVX (Sula et al., 2017) | None | 145 × 145 × 120 | 209,838 | 400 ns |
| GLIC | 4NPQ (Sauguet et al., 2014) | None | 110 × 110 × 145 | 159,083 | 1 µs |
| TWIK-1 | 3UKM (Miller and Long, 2012) | Disulfide bond between C78 and C78 (intersubunit) | 105 × 105 × 125 | 127,219 | 200 ns |
| Cx26 | 2ZW3 (Maeda et al., 2009) | Disulfide bonds between C45 and C156, C50 and C152, C56 and C145 | 130 × 130 × 122 | 189,168 | 200 ns |
| VDAC1 | 3EMN (Ujwal et al., 2008) | None | 85 × 85 × 85 | 54,590 | 200 ns |
| TRPV1b | 3J5R (Cao et al., 2013; Liao et al., 2013; Kasimova et al., 2018) | None | 160 × 140 × 175 | 402,346 | 750 ns |
| ClC1 | 6COY (Park and MacKinnon, 2018) | None | 120 × 120 × 100 | 149,529 | 200 ns |
| M2 receptor | 3UON (Haga et al., 2012) | Disulfide bonds between C96 and C176, C413 and C416 | 90 × 90 × 105 | 76,169 | 200 ns |
| Na+/K+ ATPasec | 3WGU (Kanai et al., 2013) | D195, E358, E779, D804, and E954 are protonated; disulfide bonds between C126 and C149, C159 and C175, C213 and C276 | 115 × 115 × 175 | 250,192 | 100 ns |
The trajectory used for the analysis was taken from Yazdi et al. (2016).
The trajectory for the closed capsaicin-bound state of TRPV1 used for the analysis was taken from Kasimova et al. (2018).
The trajectory for the sodium-bound Na+/K+ ATPase used for the analysis was taken from Razavi et al. (2017).