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 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 Career Guide How to Apply for a Bioinformatics PhD in India and Abroad: Eligibility, Funding and Timeline Compare the Indian, US and European PhD routes, check your eligibility, find who funds you, and start the cycle early enough to… Ragini Mishra 17 min read Drug Design Why AutoDock Vina Gives Different Results Every Time (Exhaustiveness, Seed and Reproducible Docking) Vina's search is non-deterministic, so scores shift between runs. Learn what exhaustiveness controls, how --seed fixes it, and how to report both. Dr. Abdul Rajjak Shaikh 11 min read Molecular Modeling How to Run GROMACS on an HPC Cluster with SLURM: Job Scripts, Modules and Restarts Move your GROMACS run from a laptop to a shared cluster. Load the right module, write a correct sbatch script, and restart… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Run an MD Simulation of a Vaccine Construct-TLR Complex in GROMACS: Setup, Length and What to Report Take a docked vaccine construct into GROMACS: which pose to carry forward, force field and box setup, how many replicas to run,… Ragini Mishra 17 min read
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