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 How to Run an MD Simulation of DNA or RNA in GROMACS Learn exactly what changes when you simulate a nucleic acid instead of a protein in GROMACS: force field, ions, box and analysis. Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How Many Replicate MD Simulations Should You Run? Learn why one trajectory is not enough, how many replicas an MSc project needs, and how to run and report them in… Dr. Abdul Rajjak Shaikh 11 min read Bioinformatics How to Predict IFN-gamma, IL-4 and IL-10 Inducing Epitopes Screen your shortlisted MHC class II binders for IFN-gamma, IL-4 and IL-10 induction, and learn when a high score is a reason… Ragini Mishra 15 min read Molecular Modeling How to Write a Molecular Docking and MD Results Section Report docking and MD results the way examiners expect: the affinity table, the redocking control, which plots earn a figure, and standalone… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Dock a Ligand to DNA or RNA (rDock and Vina) Dock a small molecule to a DNA duplex or an RNA riboswitch: receptor prep, box placement, real rDock commands, and when Vina… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling PyMOL Commands for Docking and MD: Beginner Cheat Sheet Learn the PyMOL commands docking and MD students use every week, from binding-site selections to polar contacts and ray-traced figures. Start here. Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Pick the Best Compound After Docking and MD Stop ranking hits on the Vina score alone. Build a defensible shortlist using ligand efficiency, filters and four MD criteria your examiner… Dr. Abdul Rajjak Shaikh 10 min read Career Guide How to Move Into Computational Biology From the Wet Lab Move from bench work into computational biology by re-analysing the data you already own. Follow the four moves, with a worked script. Ragini Mishra 16 min read Molecular Modeling ESMFold Tutorial: Predict Protein Structure in Seconds Fold a protein sequence with ESMFold in one curl command, read its pLDDT scores correctly, and learn when to use AlphaFold instead. Dr. Abdul Rajjak Shaikh 12 min read Bioinformatics Epitope Conservancy Analysis: A Step-by-Step Guide Run an epitope conservancy analysis across strains and variants, pick a defensible identity threshold, and learn the inverse host-proteome test. Ragini Mishra 16 min read
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