quasi-exact
Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Openbabel 2.3.2
Pymol 1.7.4.5 edu
Omega2 2.5.1.4
Python 2.7.11
Matplotlib 1.5.1
Scipy 0.17.0
Click 6.6
Default parameters were used for each software.
For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Each compound was then docked to the corresponding receptor structure with docking box defined by the cocrystal ligand. The best pose or poses were then selected by hand from highest scored poses. The quasi-exact method as described in https://doi.org/10.1093/bioinformatics/btp664 was then applied to each compound to calculate free energy of binding.
dock_close
Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Openbabel 2.3.2
Pymol 1.7.4.5 edu
Omega2 2.5.1.4
Python 2.7.11
Matplotlib 1.5.1
Scipy 0.17.0
Click 6.6
Default parameters used for all programs.
Publically available holo structures of FXR were obtained from the pdb and then aligned to the apo FXR structure provided.
Default parameters used for all programs.
For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Each compound was then docked to the corresponding receptor structure with docking box defined by the cocrystal ligand. The best pose or poses were then selected by hand from highest scored poses.