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 iMODS Tutorial: Normal Mode Analysis Step by Step Run iMODS normal mode analysis on a protein or docked complex, read every plot correctly, and avoid the input traps. Follow the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling Template Selection for Homology Modelling: A Guide Learn to find and rank homology modelling templates with BLASTp, HHpred and SWISS-MODEL using identity, coverage, resolution and state. Start here. Dr. Abdul Rajjak Shaikh 11 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 132 Close by 9 November 2026 132 funding deadlines close by 9 November 2026 and 100 of them by 2 November. New this week: Crick clinical fellowships, the… Dr. Abdul Rajjak Shaikh 81 min read Molecular Modeling Contact Map Analysis in GROMACS with gmx mdmat Build a residue contact map from a GROMACS trajectory with gmx mdmat, then a contact-frequency heatmap in MDAnalysis. Compare wild type and… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling PDBePISA Tutorial: Analyse a Protein-Protein Interface Run PDBePISA on a crystal or docked complex, read interface area, ΔiG, P-value, H-bonds and CSS, and report them correctly. Follow the… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Dock a Ligand into an AlphaFold Model, Step by Step Turn an AlphaFold model into a docking receptor you can defend: trim, superpose, check the pocket, redock a control. Follow the steps. Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Electrostatic Surface in PyMOL with APBS: Step by Step Colour a protein surface by electrostatic potential with PDB2PQR, APBS and PyMOL, or ChimeraX coulombic, and fix the usual errors. Follow the… Dr. Abdul Rajjak Shaikh 14 min read Drug Design Protein-Ligand Complex PDB from an AutoDock Vina Pose Turn the top AutoDock Vina pose into one clean protein-ligand complex PDB for GROMACS and figures, and fix the errors that follow.… Dr. Abdul Rajjak Shaikh 12 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 136 Close by 2 November 2026 136 funding deadlines close by 2 November 2026 and eleven close today. New this week: 28 FAPESP fellowship vacancies in Sao Paulo,… Dr. Abdul Rajjak Shaikh 89 min read Molecular Modeling GROMACS Topology File Explained: topol.top and .itp Files Read topol.top line by line, place ligand .itp files in the right order and fix the grompp topology errors students hit most.… Dr. Abdul Rajjak Shaikh 14 min read
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