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 Predict a Protein-Protein Complex with AlphaFold-Multimer in ColabFold (Step by Step) Learn how to model a protein-protein complex free in ColabFold, set the chain break correctly, and judge ipTM, pTM and PAE before… Dr. Abdul Rajjak Shaikh 13 min read Bioinformatics How to Run an IEDB Population Coverage Analysis for Your Epitope Set Run the IEDB Population Coverage tool step by step, format the input correctly, read PC90 properly, and fix thin coverage in South… Ragini Mishra 13 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 Career Guide Bioinformatics vs Computational Biology vs Biotechnology: Which Should You Study? Compare bioinformatics, computational biology, and biotechnology by what you do all day, then choose your degree, electives, and first project. Ragini Mishra 12 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 Bioinformatics How to Codon Optimize a Vaccine Construct for E. coli Expression: Codon Usage, CAI and Restriction Sites Learn how to codon optimize a multi-epitope vaccine construct for E. coli: reverse translation, CAI, GC3 and the restriction-site check before you… Ragini Mishra 15 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 Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 38 Close by 15 September 2026 205 life science funding calls, every one verified on the funding organisation's own page. Eight close today, thirty more by 15 September,… Dr. Abdul Rajjak Shaikh 49 min read Updated 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
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