Tag
Molecular Docking
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 Molecular Modeling How to Extract a Single Chain from a PDB File Pull one chain out of a multi-chain structure with PyMOL, ChimeraX, Biopython or the command line, then check it survives pdb2gmx. Start… Dr. Abdul Rajjak Shaikh 13 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