Table 2 The comparison of Potential of Mean Force profiles obtained from ASMD simulations and energy profiles from single structure or averaged CaverDock calculations over snapshots from MD simulations
Case | Enzyme | Ligand | Number of tunnels | Match with static CaverDock | Match with averaged CaverDock |
|---|---|---|---|---|---|
System #1 (PDB ID 1OTW) | Pyrroloquinoline–quinone synthase | Pyrrolo-quinoline quinone | 3 | 1 out of 3 | 1 out of 3 |
System #2 (PDB ID 2BFN) | Haloalkane dehalogenase LinB | trans-3-Chloro-2-propene-1-ol | 3 | 3 out of 3 | 3 out of 3 |
System #3 (PDB ID 2RFY) | Cellobiohydrolase | Cellobiose | 3 | 0 out of 3 | 1 out of 3 |
System #4 (PDB ID 2UWH) | Cytochrome P450 BM3 | 11,14,15-Trihydroxyicosatrienoic acid | 3 | 2 out of 3 | 3 out of 3 |
System #5 (PDB ID 4E2Z) | C-3′-methyltransferase | Se-adenosyl-l-selenohomocysteine | 3 | 3 out of 3 | 3 out of 3 |
System #6 (PDB ID 5EDT) | Cytochrome P450 CYP121 | (4S)-4-(5,5-Dimethylcyclohex-1-en-1-yl) cyclohex-1-ene-1-carboxylate | 4 | 0 out of 4 | 0 out of 4 |
System #7 (PDB ID 3ORW) | Phosphotriesterase | N-(6-Aminohexanoyl)-6-aminohexanoate | 2 | 2 out of 2 | 2 out of 2 |
System #8 (PDB ID 5U6M) | UDP-glucosyltransferase | Uridine 5′-diphosphate | 3 | 3 out of 3 | 3 out of 3 |