Tag
Molecular Docking
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 Molecular Modeling How to Write a Molecular Docking and MD Results Section Report docking and MD results the way examiners expect: the affinity table, the redocking control, which plots earn a figure, and standalone… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Dock a Ligand to DNA or RNA (rDock and Vina) Dock a small molecule to a DNA duplex or an RNA riboswitch: receptor prep, box placement, real rDock commands, and when Vina… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling PyMOL Commands for Docking and MD: Beginner Cheat Sheet Learn the PyMOL commands docking and MD students use every week, from binding-site selections to polar contacts and ray-traced figures. Start here. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Pick the Best Compound After Docking and MD Stop ranking hits on the Vina score alone. Build a defensible shortlist using ligand efficiency, filters and four MD criteria your examiner… Dr. Abdul Rajjak Shaikh 10 min read Molecular Modeling AlphaFold pLDDT and PAE Scores: Is Your Model Good Enough? Read pLDDT from the B-factor column and the PAE plot, then apply a clear go/no-go rule for docking or MD. Learn which… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Energy-Minimize a Ligand in Avogadro Before Docking Build, protonate and energy-minimize a ligand in Avogadro, then export a clean file for Vina. Follow the steps and avoid the mistakes… Dr. Abdul Rajjak Shaikh 12 min read