Latest guide
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
Guides and tutorials
Computational life sciences, explained step by step.
Real commands, real parameters, and the errors that actually catch people out. Written by researchers who use these tools.
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 Drug Design Protein-Ligand Complex PDB from an AutoDock Vina Pose Turn the top AutoDock Vina pose into one clean protein-ligand complex PDB for GROMACS and figures, and fix the errors that follow.… Dr. Abdul Rajjak Shaikh 12 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 136 Close by 2 November 2026 136 funding deadlines close by 2 November 2026 and eleven close today. New this week: 28 FAPESP fellowship vacancies in Sao Paulo,… Dr. Abdul Rajjak Shaikh 89 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 Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 76 Close by 26 October 2026 Seventy-six funding deadlines close by 26 October 2026, seventeen of them on 15 October. New this week: five Aarhus PhD calls, six… Dr. Abdul Rajjak Shaikh 64 min read
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