Tag
Drug Design
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 Molecular Modeling How to Choose a Protein Target and Ligands for a Molecular Docking Study (Step-by-Step) Pick a defensible protein target and ligand set before you open AutoDock Vina. Follow the step-by-step selection checklist that survives a viva. Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Make Publication-Quality Figures in PyMOL: Protein-Ligand Complexes, Step by Step 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… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Calculate Protein-Ligand Binding Free Energy in GROMACS (MM-PBSA Tutorial) 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. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling How to Do Blind Docking with AutoDock Vina When You Don’t Know the Binding Site Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses.… Dr. Abdul Rajjak Shaikh 11 min read Updated Drug Design AutoDock Vina vs AutoDock4: Which Docking Tool Should a Beginner Use? Compare AutoDock Vina and AutoDock4 on scoring, speed, setup, and accuracy so you pick the right docking engine for your thesis. Read… Dr. Abdul Rajjak Shaikh 9 min read Updated