Tag
Molecular Docking
Molecular Modeling How to Convert Molecular File Formats with Open Babel (PDB to PDBQT, MOL2 and SDF): A Beginner’s Guide Learn to convert PDB to PDBQT, MOL2, SDF and SMILES with Open Babel and get your docking files ready today. Dr. Abdul Rajjak Shaikh 9 min read Updated Molecular Modeling Molecular Docking vs Molecular Dynamics: What’s the Difference, and Do You Need Both? Compare molecular docking and molecular dynamics: what a pose proves, what a trajectory adds, and why a defensible thesis project runs both… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Choose a Protein Target and Ligands for a Molecular Docking Study (Step-by-Step) Pick a defensible protein target and ligand set before you open AutoDock Vina. Follow the step-by-step selection checklist that survives a viva. Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Make Publication-Quality Figures in PyMOL: Protein-Ligand Complexes, Step by Step Turn a docked pose into a figure your supervisor accepts. Real PyMOL commands for cartoon-plus-sticks, labelled H-bonds, and a 300 dpi ray-traced… Dr. Abdul Rajjak Shaikh 13 min read Updated Molecular Modeling How to Do Blind Docking with AutoDock Vina When You Don’t Know the Binding Site Learn to run blind docking in AutoDock Vina to find an unknown binding site, from sizing a whole-protein box to clustering poses.… Dr. Abdul Rajjak Shaikh 11 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 Molecular Modeling AlphaFold vs Homology Modelling vs Experimental Structures: Which to Use, When Learn to choose between an experimental PDB structure, a SWISS-MODEL homology model, or AlphaFold for docking and MD, judged on coverage, confidence… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Write the Methods Section for a Molecular Docking Study Write a docking methods section a reviewer accepts. Get the reporting checklist plus a worked, copy-adaptable AutoDock Vina example. Dr. Abdul Rajjak Shaikh 10 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