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 and AutoDock Vina on Mac: Apple Silicon Setup Install GROMACS, AutoDock Vina, Open Babel and PyMOL natively on an Apple Silicon Mac. No Rosetta, no MGLTools. Follow the verified setup. Dr. Abdul Rajjak Shaikh 13 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 64 Close by 28 September 2026 Sixty-four funding deadlines close by 28 September 2026, ten of them today. Sixty-one entries are new since last week, most of them… Dr. Abdul Rajjak Shaikh 47 min read Molecular Modeling SwissDock Tutorial: Dock a Ligand to a Protein Online Dock a ligand to a protein in your browser with SwissDock: pick AC or Vina, set the box, read the scores. Follow… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling Protein-Ligand Interaction Energy in GROMACS (Rerun Guide) Compute Coulomb and LJ protein-ligand interaction energy in GROMACS with energygrps, mdrun -rerun and gmx energy. Follow the exact commands. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling gmx make_ndx Tutorial: Index Groups for Protein-Ligand MD Build Protein_LIG, ligand heavy-atom and pocket index groups with gmx make_ndx, script them, and fix the grompp group errors. Follow each step. Dr. Abdul Rajjak Shaikh 15 min read Molecular Modeling Set Up WSL2 for GROMACS, Vina and Open Babel Install WSL2 on Windows and get GROMACS, AutoDock Vina and Open Babel running in one Ubuntu shell. Follow every command, path and… Dr. Abdul Rajjak Shaikh 14 min read Bioinformatics How to Select Target Antigens for Reverse Vaccinology Start a vaccine design project right. Five filters, in order, that cut a whole proteome down to the proteins worth predicting epitopes… Ragini Mishra 11 min read Career Guide How to Find a Bioinformatics Internship: BSc and MSc Four real routes into a bioinformatics internship, what each one asks of you, and how to write the email most students never… Ragini Mishra 15 min read Molecular Modeling MODELLER Tutorial: Build a Homology Model Step by Step Install MODELLER, pick a template, write the align2d alignment, run AutoModel and rank your models by DOPE score, using the official tutorial… Dr. Abdul Rajjak Shaikh 16 min read Bioinformatics ProtParam for a Vaccine Construct: Reading Every Number Run ProtParam on your multi-epitope construct and learn what each number means, which cutoff is real, and what to change when a… Ragini Mishra 16 min read
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