Docking and Scoring in
Discovery Studio- Training

Overview - Docking & Scoring win Discovery Studio - Training

In this workshop the Ligand Docking, Scoring and Pose Analysis protocols available in Discovery Studio are discussed.

On completion of the workshop the user will have covered:

• Use of the Binding Site tool panel to define a binding site using receptor cavities or known ligands for use in the Receptor-Ligand Interactions protocols
• Preparation of large libraries of ligands for docking and other molecular modeling workflows and protocols
• Setting up and running a docking protocol using LigandFit and analyze the poses
• Computing scores for docked poses using the following scoring algorithms: LigScore1 and LigScore2, PLP1 and PLP2, Jain, PMF, Ludi scores.
• Performing consensus scoring
• Energy-minimizing the docked ligand poses within the receptor
• Using the CDOCKER protocol to run a CHARMm-based molecular dynamics algorithm to dock ligands into a receptor
• Computing the binding energy between a receptor and a series of ligands using CHARMm
• Using the Analyze Ligand Poses protocol to compute RMSD between different ligand poses, and calculate number of hydrogen bonds and Contacts between ligand poses and a receptor
• Using Discovery Studio as an interface for running the GOLD (Genetic Optimization for Ligand Docking) program