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
AMBER14
Default parameters were used for each software.
Compounds were edited into the crystal structure for FXR_17. AMBER force field parameters were then generated for each compound in the set and MD simulations were run for each compound in the FXR_17 receptor. Simulations were analyzed to determine important bond stabilities for each compound. 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.