Table 2.
Union of the top 10 submissions by both median and mean RMSD of Pose 1, for the pose prediction component of the challenge, including only submissions that include the full set of ligands. (a) Results based on all ligands. (b) Results based only on ligands with Tanimoto similarities < 0.3 with ligands in publicly available FXR co-crystal structures; i.e., the isoxazoles (FXRs 4 and 23), spirocycles (FXRs 10, 11, and 12), tetrahydropyrro(azo)lopyridines (FXRs 15, 16, and 17), and other unclassified ligands (FXRs 1, 2, 3, and 18). Methods are listed in order of increasing mean RMSD.
| (a) | |||||
|---|---|---|---|---|---|
| Mean RMSD | Median RMSD | Software Used | Submitter Name | Group/PI Name | Receipt ID |
| 1.95 | 1.17 | Molsoft ICM | Polo Lam | Max Totrov | ixnzu |
| 2.12 | 1.27 | Autodock Vina, GROMACS, in-house LIE (Linear Interaction Energy Model) | Oleksandr Yakovenko | Steve Jones | txyzj |
| 2.19 | 1.02 | GLIDE, CCDC-GOLD, Amber14, MMGBSA | Yuan Hu | Merck | 7ltmc |
| 2.19 | 1.13 | Glide, Gold, Induced-fit-docking | Hongwu Wang | Merck | hciq4 |
| 2.27 | 1.39 | Wilma (flexible ligand docking algorithm), scoring function SIE (force field based scoring function) | Enrico Purisima | Enrico Purisima | jz0em |
| 2.34 | 0.99 | WaterMap, SHAPE Screening, Structural Interaction Fingerprint, DFT/B3LYP/6-31G*, GLIDE-SP-XP, Induced-fit-docking, Emodel/GlideScore-SP, Binding Pose Metadynamics | Christina Athanasiou | Zoe Cournia | oky3v |
| 2.37 | 1.16 | Glide-XP | Anonymous | Anonymo us | cfn8u |
| 2.76 | 1 | OMEGA, SHAFTS, NoDocking, Amber11 | Xiaoqin Zou | Xiaoqin Zou | mgxbc |
| 2.76 | 1.2 | Modeller, Gromacs (minimization), surflex-sim, Clusterizer and DockAccessor, Vina | Flavio Ballante | Garland R. Marshall | 5cf33 |
| 2.92 | 1.19 | ROCS, Omega, Glide-SP-XP | Ashutosh Kumar | Kam Y.J. Zhang | 5rqrx |
| 3.08 | 1.2 | MOE (most similar molecule), Confgen, Forge (alignment), Smina (minimization), Manual ranking | Matthew Baumgartner | David Evans | wax1j |
| 3.16 | 1.2 | Forge, Smina (minimization only), Glide-SP | Matthew Baumgartner | David Evans | psiuj |
| (b) | |||||
|---|---|---|---|---|---|
| Mean RMSD | Median RMSD | Software Used | Submitter Name | Group/PI Name | Receipt ID |
| 3.65 | 2.6 | Autodock Vina, GROMACS, in-house LIE (Linear Interaction Energy Model) | Oleksandr Yakovenko | Steve Jones | txyzj |
| 3.66 | 2.72 | Molsoft ICM | Maxim Totrov | Max Totrov | ixnzu |
| 4.02 | 3.74 | Smina, idock-RF-v3, Yasara (simulated annealing) | Yuan Hu | Merck | 7ltmc |
| 4.24 | 3.75 | Glide, Gold, Induced-fit-docking | Hongwu Wang | Merck | hciq4 |
| 4.25 | 3.06 | Wilma (flexible ligand docking algorithm), scoring function SIE (force field based scoring function) | Enrico Purisima | Enrico Purisima | jz0em |
| 4.54 | 3.85 | Glide-XP | Anonymous | Anonymous | cfn8u |
| 4.76 | 5.66 | WaterMap, SHAPE Screening, Structural Interaction Fingerprint, DFT/B3LYP/6-31G*, GLIDE-SP-XP, Induced-fit-docking, Emodel/GlideScore-SP, Binding Pose Metadynamics | Christina Athanasiou | Zoe Cournia | oky3v |
| 4.79 | 4.26 | Smina | Bentley Wingert | Carlos Camacho | 6tnqb |
| 4.79 | 4.26 | Smina | Bentley Wingert | Carlos Camacho | h67ea |
| 4.88 | 5.16 | Induced-fit-docking | Anonymous | Anonymous | piwli |
| 4.94 | 4.25 | Modeller, Gromacs (minimization), surflex-sim, Clusterizer and DockAccessor, Vina | Flavio Ballante | Garland R. Marshall | 5cf33 |
| 5.26 | 4.73 | AutoDock Vina, Gromacs | Pär Söderhjelm | Soderhjelm Research Group | byf51 |