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 Define the Simulation Box in GROMACS with gmx editconf (Cubic vs Dodecahedron): A Step-by-Step Guide Set your GROMACS simulation box with gmx editconf. Choose cubic or dodecahedron, pick the right -d distance, and cut roughly 29 percent… Dr. Abdul Rajjak Shaikh 13 min read Updated Career Guide Bioinformatics Career Paths and Job Roles, Explained for BSc and MSc Students The seven bioinformatics job families that actually hire, the stack each one screens on, and the single project that proves you can… Ragini Mishra 13 min read Molecular Modeling How to Find a Protein’s Binding Site for Docking with fpocket, CASTp and PrankWeb Predict a protein's binding pocket with PrankWeb, fpocket or CASTp, then convert it into the grid box coordinates AutoDock Vina needs. Dr. Abdul Rajjak Shaikh 15 min read Updated Molecular Modeling How to Use gmx cluster: Extract a Representative Structure from a GROMACS Trajectory Learn to run gmx cluster with the gromos method and pull one defensible representative structure from your GROMACS trajectory. Dr. Abdul Rajjak Shaikh 10 min read Updated Bioinformatics How to Predict T-Cell Epitopes and MHC Binding with NetMHCpan and IEDB Pick an HLA panel, set the right peptide length, and filter on percentile rank. Turn thousands of NetMHCpan rows into a defensible… Ragini Mishra 17 min read Molecular Modeling How to Use gmx trjconv: Fix PBC and Extract Frames from a GROMACS Trajectory Learn the exact gmx trjconv commands to remove PBC artifacts, center your protein, strip water, and extract single frames before you run… Dr. Abdul Rajjak Shaikh 10 min read Updated Career Guide Fully Funded Life Science PhD, Fellowship and Scholarship Deadlines: August 2026 Onwards 90 life science PhD, fellowship and scholarship deadlines, every one verified on the funding organisation's official page. Africa and Latin America are… Dr. Abdul Rajjak Shaikh 95 min read Updated Molecular Modeling How to Generate a GROMACS Topology with pdb2gmx: A Step-by-Step Beginner’s Guide Learn to run gmx pdb2gmx step by step, pick a force field and water model, and fix the "residue not found" error… Dr. Abdul Rajjak Shaikh 8 min read Updated Bioinformatics How to Download a Protein Structure from the RCSB PDB and Read the File Find, download, and actually read a protein structure from the RCSB PDB before you dock or run MD. Start your modelling workflow… Dr. Abdul Rajjak Shaikh 9 min read Updated Career Guide How to Become a Bioinformatician in India After BSc or MSc: A Practical Roadmap Four real routes into bioinformatics after a BSc or MSc in India, the exams that fund them, and the skills a hiring… Ragini Mishra 15 min read
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