jz0em-PosePredictionProtocol.txt

Name

Wilma/SIE Method 1

Software

Wilma/SIE

System Preparation Parameters

Assumed pH 7.4

System Preparation Method

Multiple protein crystal structures used. Water and ions removed. 3D structures of ligands constructed in MOE. Ligand charging method AM1BCC. Protein hydrogen atoms and capping groups for chain termini and broken chains added in MOE. Protein charging using AMBER. Protein refinement by constrained minimization with the AMBER force field (also used for complex relaxation after docking).

Pose Prediction Parameters

Default docking and relaxation parameters. Standard parameterization of the Wilma and SIE scoring functions were employed. Method described in Hogues et al. JCIM 2016, 56:1292-303.

Pose Prediction Method

Wilma is an exhaustive flexible-ligand docking algorithm that uses its own scoring function to narrow down the number of feasible ligand poses against a protein surface. The force-field based scoring function SIE is then used to locate the best scoring pose. Details are given in Hogues et al. JCIM 2016, 56:1292-303 and references cited therein.