Topic
Drug Design
Drug Design Why AutoDock Vina Gives Different Results Every Time (Exhaustiveness, Seed and Reproducible Docking) Vina's search is non-deterministic, so scores shift between runs. Learn what exhaustiveness controls, how --seed fixes it, and how to report both. Dr. Abdul Rajjak Shaikh 11 min read Drug Design How to Check Drug-Likeness and ADMET of Your Docked Ligands (SwissADME, pkCSM and Lipinski’s Rule of Five) Learn to run SwissADME and pkCSM on your top docking hits, read the BOILED-Egg, and report Lipinski violations correctly in your thesis. Dr. Abdul Rajjak Shaikh 12 min read Updated Drug Design AutoDock Vina vs AutoDock4: Which Docking Tool Should a Beginner Use? Compare AutoDock Vina and AutoDock4 on scoring, speed, setup, and accuracy so you pick the right docking engine for your thesis. Read… Dr. Abdul Rajjak Shaikh 9 min read Updated Drug Design How to Make 2D Protein-Ligand Interaction Diagrams (LigPlot+ & PLIP): Step by Step Turn any AutoDock Vina or PyRx docking pose into a publication-ready 2D interaction diagram with free tools. Follow the LigPlot+ and PLIP… Dr. Abdul Rajjak Shaikh 9 min read Updated Drug Design 7 Molecular Docking Project Ideas for Your MSc Thesis (and Your CV) Pick a scoped, defensible molecular docking project you can finish with free tools and public data. Start building your thesis today. Dr. Abdul Rajjak Shaikh 7 min read Updated