Tag
Molecular Docking
Molecular Modeling PDB File Format Explained: ATOM, HETATM and Every Column Learn to read a PDB file column by column, from altLocs to B-factors, and fix the five format faults that break docking… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling Vina Scoring Functions: Vina vs Vinardo vs AD4 (–scoring) Vina, Vinardo or AD4? Learn what the --scoring flag changes, the exact command for each, and how to test them by redocking.… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling iMODS Tutorial: Normal Mode Analysis Step by Step Run iMODS normal mode analysis on a protein or docked complex, read every plot correctly, and avoid the input traps. Follow the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Dock a Ligand into an AlphaFold Model, Step by Step Turn an AlphaFold model into a docking receptor you can defend: trim, superpose, check the pocket, redock a control. Follow the steps. Dr. Abdul Rajjak Shaikh 13 min read Drug Design Protein-Ligand Complex PDB from an AutoDock Vina Pose Turn the top AutoDock Vina pose into one clean protein-ligand complex PDB for GROMACS and figures, and fix the errors that follow.… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Meeko Tutorial: Prepare Ligands and Receptors for Vina Prepare ligands and receptors for AutoDock Vina with Meeko. Learn mk_prepare_ligand, mk_prepare_receptor and mk_export with real commands and fixes. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Extract a Ligand from a PDB File (PyMOL, ChimeraX) Pull the bound ligand out of a PDB complex, restore its bond orders and hydrogens, and use it to centre your docking… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling GNINA Docking Tutorial: CNN Scoring After AutoDock Vina Run your first GNINA docking job, read CNNscore and CNNaffinity correctly, and rescore your Vina poses. Follow the step-by-step commands. Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Covalent Docking Tutorial: Dock a Covalent Inhibitor AutoDock Vina cannot dock covalent inhibitors. Compare the free routes, run a covalent job in ADFR step by step, and validate the… Dr. Abdul Rajjak Shaikh 16 min read Updated Molecular Modeling DockingPie Tutorial: Molecular Docking in PyMOL Run Smina, AutoDock Vina, ADFR and RxDock from inside PyMOL with no terminal. Install DockingPie, dock your first ligand and compare engines. Dr. Abdul Rajjak Shaikh 15 min read