Drug Design

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.

Estimate protein-ligand binding free energy from a finished GROMACS trajectory with the free gmx_MMPBSA tool. Follow the step-by-step MM-PBSA workflow now.

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.

Compare AutoDock Vina and AutoDock4 on scoring, speed, setup, and accuracy so you pick the right docking engine for your thesis. Read the guide before you start.

Write a docking methods section a reviewer accepts. Get the reporting checklist plus a worked, copy-adaptable AutoDock Vina example.

Pick a scoped, defensible molecular docking project you can finish with free tools and public data. Start building your thesis today.

Set the AutoDock Vina grid box the right way: find the binding-site center, pick a box size in Angstroms, and stop guessing coordinates. Start docking today.