Molecular Docking

Stop running Vina once per compound. Learn the –batch flag, the Open Babel prep loop, and how to pull 40 output files into one ranked table.

Learn to run SwissADME and pkCSM on your top docking hits, read the BOILED-Egg, and report Lipinski violations correctly in your thesis.

Dock two proteins in a browser with ClusPro, HDOCK or HADDOCK. Prepare your files, run the job, and learn which model to keep and why.

Predict a protein’s binding pocket with PrankWeb, fpocket or CASTp, then convert it into the grid box coordinates AutoDock Vina needs.

Find, download, and actually read a protein structure from the RCSB PDB before you dock or run MD. Start your modelling workflow the right way.

Learn to convert PDB to PDBQT, MOL2, SDF and SMILES with Open Babel and get your docking files ready today.

Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both in order.

Pick a defensible protein target and ligand set before you open AutoDock Vina. Follow the step-by-step selection checklist that survives a viva.

Turn a docked pose into a figure your supervisor accepts. Real PyMOL commands for cartoon-plus-sticks, labelled H-bonds, and a 300 dpi ray-traced render.

Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses. Start the step-by-step guide.