Tag
Drug Design
Drug Design Why AutoDock Vina Gives Different Results Every Time (Exhaustiveness, Seed and Reproducible Docking) Vina's search is non-deterministic, so scores shift between runs. Learn what exhaustiveness controls, how --seed fixes it, and how to report both. Dr. Abdul Rajjak Shaikh 11 min read Molecular Modeling How to Install AutoDock Vina on Windows 10 and 11: A Step-by-Step Guide for Beginners (Vina 1.2.7 + AutoDockTools) Install AutoDock Vina 1.2.7 on Windows the way it ships today: one bare .exe, no MSI, plus MGLTools for AutoDockTools. Follow the… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Analyze Protein-Ligand Interactions Over an MD Trajectory (ProLIF and MDAnalysis, Step by Step) Compute which binding-site residues held your ligand and for what percentage of the run, using ProLIF and MDAnalysis on a PBC-corrected GROMACS… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Do Flexible Docking in AutoDock Vina (Flexible Side Chains, Step by Step) Learn how to let binding-site side chains move in AutoDock Vina: split the receptor with Meeko, run vina --flex, and judge whether… Dr. Abdul Rajjak Shaikh 14 min read Updated Molecular Modeling How to Calculate a Binding Free Energy with Umbrella Sampling in GROMACS (Pulling, Windows and gmx wham) Learn how to run umbrella sampling in GROMACS: set up the pull code, pick windows that overlap, run gmx wham and read… Dr. Abdul Rajjak Shaikh 18 min read Updated Molecular Modeling How to Dock Multiple Ligands in AutoDock Vina (Batch Docking): A Step-by-Step Guide Stop running Vina once per compound. Learn the --batch flag, the Open Babel prep loop, and how to pull 40 output files… Dr. Abdul Rajjak Shaikh 17 min read Updated Drug Design How to Check Drug-Likeness and ADMET of Your Docked Ligands (SwissADME, pkCSM and Lipinski’s Rule of Five) Learn to run SwissADME and pkCSM on your top docking hits, read the BOILED-Egg, and report Lipinski violations correctly in your thesis. Dr. Abdul Rajjak Shaikh 12 min read Updated Molecular Modeling How to Find a Protein’s Binding Site for Docking with fpocket, CASTp and PrankWeb Predict a protein's binding pocket with PrankWeb, fpocket or CASTp, then convert it into the grid box coordinates AutoDock Vina needs. Dr. Abdul Rajjak Shaikh 15 min read Updated Molecular Modeling How to Convert Molecular File Formats with Open Babel (PDB to PDBQT, MOL2 and SDF): A Beginner’s Guide Learn to convert PDB to PDBQT, MOL2, SDF and SMILES with Open Babel and get your docking files ready today. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Molecular Docking vs Molecular Dynamics: What’s the Difference, and Do You Need Both? Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both… Dr. Abdul Rajjak Shaikh 11 min read Updated