Tag
Molecular Docking
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 Molecular Modeling Discovery Studio Visualizer Tutorial: How to Analyse Docking Results and Make 2D Interaction Diagrams Load your docked pose, list every contact with its distance, and export the 2D interaction diagram your thesis needs. Follow the full… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Do Ensemble Docking with MD Snapshots (Receptor Flexibility Beyond Flexible Side Chains) Learn ensemble docking step by step: run MD on the apo protein, cluster the trajectory, dock into every snapshot, then combine the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Dock a Peptide to a Protein (HPEPDOCK, HADDOCK and AutoDock CrankPep): A Step-by-Step Guide Learn peptide-protein docking step by step with HPEPDOCK, HADDOCK and AutoDock CrankPep, and find out which one to run for your project. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Handle Metal Ions in Molecular Docking and MD (Zinc, Magnesium and Iron, Step by Step) Stop deleting the zinc. Learn when to keep a metal ion, how to dock into a metalloprotein with AutoDock4Zn, and how to… Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling How to Set Protonation States and Add Hydrogens to a Protein Before Docking or MD (PDB2PQR, PROPKA and H++) Crystal structures ship without hydrogens. Learn to predict pKa values with PROPKA, protonate with PDB2PQR or H++, and check the result before… Dr. Abdul Rajjak Shaikh 14 min read 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 Molecular Modeling How to Run an MD Simulation of a Vaccine Construct-TLR Complex in GROMACS: Setup, Length and What to Report Take a docked vaccine construct into GROMACS: which pose to carry forward, force field and box setup, how many replicas to run,… Ragini Mishra 17 min read Bioinformatics How to Get the Right Protein Sequence from UniProt for Modelling (Canonical Isoform, Signal Peptide and Residue Numbering) Pick a reviewed Swiss-Prot entry, take the canonical isoform, cut the signal peptide, and check the PDB offset before you model. Follow… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Install AutoDock Vina on Windows 10 and 11: A Step-by-Step Guide for Beginners (Vina 1.2.7 + AutoDockTools) Install AutoDock Vina 1.2.7 on Windows the way it ships today: one bare .exe, no MSI, plus MGLTools for AutoDockTools. Follow the… Dr. Abdul Rajjak Shaikh 13 min read Updated