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 Extract a Single Chain from a PDB File Pull one chain out of a multi-chain structure with PyMOL, ChimeraX, Biopython or the command line, then check it survives pdb2gmx. Start… Dr. Abdul Rajjak Shaikh 13 min read Bioinformatics Multi-Epitope Vaccine Structure: Model, Refine, Validate Model a vaccine construct with no template, read the low pLDDT at your linkers correctly, refine it, and validate it before you… Ragini Mishra 13 min read Career Guide How to Write a Bioinformatics CV as a Student Build a bioinformatics CV a reader can verify. Learn the evidence rule, rewrite weak skill lines, and see a full worked projects… Ragini Mishra 17 min read Updated Drug Design Molecular Docking of Phytochemicals: Step-by-Step Guide Build a defensible plant-compound list from IMPPAT, Dr. Duke's and COCONUT, prepare the ligands properly, and dock them with AutoDock Vina. Start… Dr. Abdul Rajjak Shaikh 16 min read 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
Weekly funding email
Get every new funding deadline by email
One email a week listing the funded PhD positions, fellowships and scholarships added that week, each one read from the funder's own website. Nothing else is sent.
Unsubscribe in one click from any email. We do not share your address, and we do not send anything else.
Learn this properly, live
A small-batch cohort in molecular modelling, docking and MD simulations, taught by researchers who publish. You run the full pipeline yourself.
See the next cohort