A hierarchical docking method: XDZ_2
AutoDock Vina 1.0/ITScore2
Gasteiger charges #Vina
Waters/cofactors in the bound protein structures were
kept for docking. Preparation for docking with Vina was done using MGLTools.
Exhaustiveness=30 #exhaustiveness of global search (default=8)
Vina scoring function (empirical + knowledge-based function)
Num_modes=500 #max number of poses to generate
Re-scoring function, ITScore2 #ITScore version 2.0
A query ligand was docked to the bound protein structure using
Vina. Waters/cofactors were considered in the dokcing process.
Upto 500 putative binding modes were generated for further evaluation.
A knowledge-based scoring function, ITScore2, was used to
evaluate these binding models. The scoring function was developed with a statistical
mechanics-based iterative method using the refined set of PDBbind 2012.
No
Yes