Secondary Screening: Vina Docking and Ranking by Binding Energy Juan C. Torres Carolina Montanez Gretel Montanez Luzmarie Reyes
ObjectiveTo perform a secondary screening to identify theusing AutoDock Vina.
Drug Discovery Strategy Biological Problem (Biomedically Relevant Condition or Process) Primary Sequence Optimal target (s) Analysis; degree for drug development conservationTherapeutically (NCBI/Swiss-Prot) FTmap Target Analysis Chemical probes Number, qualityrelevant protein cluster and distance of targets number & quality “hot spots’ Pharmacophore . 3D Structure identification and www.pdb.org PyMol Pharmacophore Model Generation (LigandScout) Primary Screening: Pharmacophore Drug-like Databases Model (≈ 9.5 million drugs) (Ligand Scout) Lead-like Database Further refinement (≈ 1.3 million drugs) of Pharmacophore Model Identification of Top Hits Secondary Screening (AutoDock) Identification of High Affinity Lead Compounds. BioAssay Lead (Ranking of binding Compounds energies)
Part 1: Run the Docking Screening (AutoDock Vina)
Part 2: Obtain the Results/ Ranking of Top Hits
Part 3: Analyze Interactions using Auto Dock tools