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 Pick the Best Compound After Docking and MD Stop ranking hits on the Vina score alone. Build a defensible shortlist using ligand efficiency, filters and four MD criteria your examiner… Dr. Abdul Rajjak Shaikh 10 min read Career Guide How to Move Into Computational Biology From the Wet Lab Move from bench work into computational biology by re-analysing the data you already own. Follow the four moves, with a worked script. Ragini Mishra 16 min read Molecular Modeling ESMFold Tutorial: Predict Protein Structure in Seconds Fold a protein sequence with ESMFold in one curl command, read its pLDDT scores correctly, and learn when to use AlphaFold instead. Dr. Abdul Rajjak Shaikh 12 min read Bioinformatics Epitope Conservancy Analysis: A Step-by-Step Guide Run an epitope conservancy analysis across strains and variants, pick a defensible identity threshold, and learn the inverse host-proteome test. Ragini Mishra 16 min read Molecular Modeling AlphaFold pLDDT and PAE Scores: Is Your Model Good Enough? Read pLDDT from the B-factor column and the PAE plot, then apply a clear go/no-go rule for docking or MD. Learn which… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Energy-Minimize a Ligand in Avogadro Before Docking Build, protonate and energy-minimize a ligand in Avogadro, then export a clean file for Vina. Follow the steps and avoid the mistakes… Dr. Abdul Rajjak Shaikh 12 min read Career Guide How to Prepare for a Bioinformatics Interview Prepare for the four assessments in a bioinformatics interview: the CV screen, the data-handling test, the project deep-dive and the biology check. Ragini Mishra 16 min read Molecular Modeling DCCM Analysis of a GROMACS Trajectory, Step by Step Compute and read a dynamic cross-correlation matrix from a GROMACS run with Bio3D, ProDy or NumPy. Follow the exact commands and fix… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Per-Residue Energy Decomposition with gmx_MMPBSA Turn one MM-GBSA number into a per-residue breakdown. Set up the decomp namelist, read the output and name your hotspot residues with… Dr. Abdul Rajjak Shaikh 15 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 87 Close by 5 October 2026 Eighty-seven funding deadlines close by 5 October 2026, fifty-three of them Indian project posts with walk-in interviews inside the next fortnight. Europe's… Dr. Abdul Rajjak Shaikh 64 min read
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