Tag
AutoDock Vina
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 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 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 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 Drug Design Molecular Docking of Phytochemicals: Step-by-Step Guide Build a defensible plant-compound list from IMPPAT, Dr. Duke's and COCONUT, prepare the ligands properly, and dock them with AutoDock Vina. Start… Dr. Abdul Rajjak Shaikh 16 min read Molecular Modeling GROMACS and AutoDock Vina on Mac: Apple Silicon Setup Install GROMACS, AutoDock Vina, Open Babel and PyMOL natively on an Apple Silicon Mac. No Rosetta, no MGLTools. Follow the verified setup. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling SwissDock Tutorial: Dock a Ligand to a Protein Online Dock a ligand to a protein in your browser with SwissDock: pick AC or Vina, set the box, read the scores. Follow… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Set Up WSL2 for GROMACS, Vina and Open Babel Install WSL2 on Windows and get GROMACS, AutoDock Vina and Open Babel running in one Ubuntu shell. Follow every command, path and… Dr. Abdul Rajjak Shaikh 14 min read