2ytv8-FreeEnergyProtocol.txt

Name

Alchemical Free Energy Calculation

Software

Gromacs, PMX

Parameter

OPLS-AA forcefield
Assumed pH 7.0
10 ns Molecular Dynamics simulations at 300 K. Integrator : sd. Berendsen pressure coupling.
Morphing : Short 50 ps MD at 300 K on 200 extracted conformations from state A and state B simulations.
Morphing : sc-alpha = 0.5, sc-sigma = 0.25.
Morphing : Integrator : md. Pressure coupling : berendsen. Temperature coupling : velocity rescale
TIP4P water molecules

Method

The protein used for free energy calculation was taken from PDB database with PDB entry corresponding to 3FLI. Ligands 3D coordinates were built using Chimera, by superimposing common backbone on released FXR_17, FXR_10 and FXR_12 structures. In the set2, the structure solved by X-ray crystallography for FXR_12 had two alternative positions for the aromatic ring substituent (AA and AB). Both of them were considered in our calculations, and the one leading to the most favorable energy chosen for the submission. Alchemical free energies were calculated using Gromacs and OPLS-AA force field, some scripts from the PMX software and some in house developed scripts. Hybrid structures and topologies were built using a modified version of the MOL2FF package developed in our team. FXR_17 was used as reference structure for set1, and FXR_10 or FXR_12 for set2. Equilibrium 10 ns MD simulations were performed for the two states (corresponding to lambda 0 and 1), using Gromacs and OPLS-AA force field. Snapshots from the equilibrium runs were extracted to spawn 100 simulations of 50 ps each to alchemically morph between the two states of the system. The work values over every non-equilibrium transition were extracted and further used to estimate the free energy differences relying on the Crooks Fluctuation Theorem and utilizing Crooks-Gaussian Intersection as estimator.

2ytv8-PosePredictionProtocol.txt

Name

D3RGC2-Free-Energy

Software

UCSF Chimera v1.10.2

System Preparation Parameters

Protonation state of ligands at pH 7.0 was considered.

System Preparation Method

The structures FXR_17, FXR_10 or FXR_12 released after Stage 1 were used as templates for building the coordinates of ligand from the two free energy datasets.

Pose Prediction Parameters

None

Pose Prediction Method

Ligands 3D coordinates were built using Chimera, by building the ligand structure starting from the structures FXR_17, FXR_10 or FXR_12 released after Stage 1.