Topic
Molecular Modeling
Molecular Modeling PDBePISA Tutorial: Analyse a Protein-Protein Interface Run PDBePISA on a crystal or docked complex, read interface area, ΔiG, P-value, H-bonds and CSS, and report them correctly. Follow the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Dock a Ligand into an AlphaFold Model, Step by Step Turn an AlphaFold model into a docking receptor you can defend: trim, superpose, check the pocket, redock a control. Follow the steps. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Electrostatic Surface in PyMOL with APBS: Step by Step Colour a protein surface by electrostatic potential with PDB2PQR, APBS and PyMOL, or ChimeraX coulombic, and fix the usual errors. Follow the… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling GROMACS Topology File Explained: topol.top and .itp Files Read topol.top line by line, place ligand .itp files in the right order and fix the grompp topology errors students hit most.… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Meeko Tutorial: Prepare Ligands and Receptors for Vina Prepare ligands and receptors for AutoDock Vina with Meeko. Learn mk_prepare_ligand, mk_prepare_receptor and mk_export with real commands and fixes. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Ramachandran Plot from a GROMACS Trajectory (gmx rama) Learn to run gmx rama on an MD trajectory, plot every frame as a phi/psi density in Python, and spot residues that… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Extract a Ligand from a PDB File (PyMOL, ChimeraX) Pull the bound ligand out of a PDB complex, restore its bond orders and hydrogens, and use it to centre your docking… Dr. Abdul Rajjak Shaikh 12 min read 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 GROMACS Protein Cofactor Simulation: Heme, NAD+ and FAD Keep heme, NAD+ or FAD in your GROMACS run: check the force field first, then parameterize only what is missing. Follow the… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Salt Bridge Analysis in GROMACS: gmx saltbr vs pairdist Track a salt bridge across a GROMACS trajectory with gmx pairdist, compute its occupancy in Python, and learn why gmx saltbr misleads.… Dr. Abdul Rajjak Shaikh 13 min read