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 Calculate Protein-Protein Binding Affinity Score your docked protein-protein complex with PRODIGY and HawkDock MM/GBSA, read dG and Kd correctly, and learn why a docking score is… Dr. Abdul Rajjak Shaikh 12 min read Molecular Modeling How to Remove Water Molecules From a PDB File for Docking Strip HOH waters and crystallisation additives from a PDB file with PyMOL, ChimeraX or pdb-tools, and learn which structural waters to keep. Dr. Abdul Rajjak Shaikh 14 min read Career Guide Free Bioinformatics Certifications Worth Doing as a Student Compare free bioinformatics certifications, see which credentials cost nothing, which charge for the certificate, and which issue none at all. Ragini Mishra 13 min read Molecular Modeling How to Dock a Ligand to a GPCR or Membrane Protein with AutoDock Vina (Step by Step) Dock a ligand into a GPCR with AutoDock Vina: pick the right activation state, strip BRIL and T4 lysozyme, and place the… Dr. Abdul Rajjak Shaikh 14 min read Career Guide Life Science PhD, Fellowship and Scholarship Deadlines: 31 Close by 21 September 2026 Thirty-one funding deadlines close by 21 September 2026, two of them today. Twenty new entries were verified this week, including ten European… Dr. Abdul Rajjak Shaikh 40 min read Molecular Modeling AutoDock Vina Errors and How to Fix Them: The 10 That Stop Beginners Decode the 10 AutoDock Vina errors that stop beginners, from PDBQT parsing failures to grid box mistakes, with the exact command that… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Predict a Protein-Protein Complex with AlphaFold-Multimer in ColabFold (Step by Step) Learn how to model a protein-protein complex free in ColabFold, set the chain break correctly, and judge ipTM, pTM and PAE before… Dr. Abdul Rajjak Shaikh 13 min read Bioinformatics How to Run an IEDB Population Coverage Analysis for Your Epitope Set Run the IEDB Population Coverage tool step by step, format the input correctly, read PC90 properly, and fix thin coverage in South… Ragini Mishra 13 min read Molecular Modeling Discovery Studio Visualizer Tutorial: How to Analyse Docking Results and Make 2D Interaction Diagrams Load your docked pose, list every contact with its distance, and export the 2D interaction diagram your thesis needs. Follow the full… Dr. Abdul Rajjak Shaikh 13 min read Career Guide Bioinformatics vs Computational Biology vs Biotechnology: Which Should You Study? Compare bioinformatics, computational biology, and biotechnology by what you do all day, then choose your degree, electives, and first project. Ragini Mishra 12 min read
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