Tag
Drug Design
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 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 Per-Residue Energy Decomposition with gmx_MMPBSA Turn one MM-GBSA number into a per-residue breakdown. Set up the decomp namelist, read the output and name your hotspot residues with… Dr. Abdul Rajjak Shaikh 15 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 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 How to Dock a Ligand to a GPCR or Membrane Protein with AutoDock Vina (Step by Step) Dock a ligand into a GPCR with AutoDock Vina: pick the right activation state, strip BRIL and T4 lysozyme, and place the… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling AutoDock Vina Errors and How to Fix Them: The 10 That Stop Beginners Decode the 10 AutoDock Vina errors that stop beginners, from PDBQT parsing failures to grid box mistakes, with the exact command that… Dr. Abdul Rajjak Shaikh 14 min read