piwli-PosePredictionProtocol.txt

Name

Colony Entropy Ensemble DOCKing

Software

Glide

System Preparation Parameters

Schrodinger Prepwizards, KEEPFARWAT, DISULFIDES, SAMPLEWATER, PROPKA 7

System Preparation Method

Schrodinger Protein Prep

Pose Prediction Parameters

MAXKEEP 6000, MAXREF 5000, POSE_DISPLACEMENT 0.0, POSE_RMSD 0.0, POSES_PER_LIG 500, POSTDOCK_NPOSE 1000, PRECISION SP, SCORING_CUTOFF 500.0

Pose Prediction Method

Ligands docked into all available pdb structures with
above parameters, poses were extracted into a single file and clustered at rmsd of 2A, clusters were scored by lowest_cluster_member_glidescore - 300*.001987*LN(clustsize), lowest energy glide score compound in best scoring cluster returned as pose.