cmv4q-PosePredictionProtocol.txt

Name

PCHD

Software

HYBRID v3.2.0.2; SMZAP 1.2.1.4

System Preparation Parameters

spruce prep -d pub_pdb -o prepped --design-ref CATS-SO4-STRUCTURE-D3R-GC3_AS__apo__SO4_S.oeb.gz --transform --split-covalent
spruce receptor --dir=prepped
omega2 -in CatS_pose_ligands_revised.smi -out CatS_pose_ligands_revised_conf.oeb.gz -maxConfRange 200,800 -rangeIncrement 8

System Preparation Method

spruce v0.7.2, omega2 v2.5.1.4

Pose Prediction Parameters

hybrid -num_poses 20 -receptor receptor.lst (60 public) -dbase CatS_pose_ligands_revised_conf.oeb.gz
szmap -protein CATS-DMSO-STRUCTURE-D3R-GC3_AF__DMS_F_apo.oeb.gz -ligand CatS_hybrid_20_poses_docked.oeb.gz -atcoords -output_mol ###.oeb.gz
szscore polcat ###.oeb.gz

Pose Prediction Method

HYBRID rescore with szscore polcat

Answer 1

Yes

Answer 2

No