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 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 Molecular Modeling gmx hbond for Protein-Ligand H-Bonds in GROMACS 2024+ Count protein-ligand hydrogen bonds with the new gmx hbond in GROMACS 2024+, or hbond-legacy. Copy the exact commands, get occupancy and read… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Ligand RMSD in GROMACS: Fit, Fix PBC, Read the Plot Calculate ligand RMSD in GROMACS the right way: fit on the protein backbone, fix periodic jumps first, and learn to read stable,… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling Covalent Docking Tutorial: Dock a Covalent Inhibitor AutoDock Vina cannot dock covalent inhibitors. Compare the free routes, run a covalent job in ADFR step by step, and validate the… Dr. Abdul Rajjak Shaikh 16 min read Updated Molecular Modeling How to Refine a Homology Model That Failed Validation Your model failed MolProbity or SAVES. Learn which refinement servers are live today, run ModRefiner step by step, and prove the fix… Dr. Abdul Rajjak Shaikh 15 min read Career Guide How to Write a Research Proposal for a Bioinformatics PhD What a bioinformatics PhD proposal has to prove, what the UGC regulations actually say about it, and how to test your own… Ragini Mishra 19 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 74 Close by 19 October 2026 Seventy-four funding deadlines close by 19 October 2026, including nine European PhD programmes and thirty-nine Indian project posts. New this week: the… Dr. Abdul Rajjak Shaikh 54 min read Molecular Modeling DockingPie Tutorial: Molecular Docking in PyMOL Run Smina, AutoDock Vina, ADFR and RxDock from inside PyMOL with no terminal. Install DockingPie, dock your first ligand and compare engines. Dr. Abdul Rajjak Shaikh 15 min read Bioinformatics How to Predict Conformational B-Cell Epitopes Run ElliPro, DiscoTope 3.0 and SEPPA 3.0 on a structure, read their scores correctly, and avoid the residue-numbering trap. Ragini Mishra 17 min read Updated
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