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How to Predict Conformational B-Cell Epitopes
Run ElliPro, DiscoTope 3.0 and SEPPA 3.0 on a structure, read their scores correctly, and avoid the residue-numbering trap.
Ragini Mishra 17 min read
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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 PyMOL vs VMD vs ChimeraX: Which Should You Learn? Pick your molecular visualization tool by the job it does. Compare PyMOL, VMD and ChimeraX on licence, platforms and scripting before you… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Wild-Type vs Mutant MD Simulation in GROMACS Design a wild-type versus mutant MD comparison in GROMACS that survives examination: matched protocol, replicas, and a difference you can defend. Dr. Abdul Rajjak Shaikh 16 min read Career Guide How to Publish Your First Bioinformatics Paper Decide whether your project is a paper, settle the author list by the ICMJE criteria, choose where to send it, and learn… Ragini Mishra 16 min read Molecular Modeling How to Run an MD Simulation of DNA or RNA in GROMACS Learn exactly what changes when you simulate a nucleic acid instead of a protein in GROMACS: force field, ions, box and analysis. Dr. Abdul Rajjak Shaikh 17 min read Updated Molecular Modeling How Many Replicate MD Simulations Should You Run? Learn why one trajectory is not enough, how many replicas an MSc project needs, and how to run and report them in… Dr. Abdul Rajjak Shaikh 11 min read Bioinformatics How to Predict IFN-gamma, IL-4 and IL-10 Inducing Epitopes Screen your shortlisted MHC class II binders for IFN-gamma, IL-4 and IL-10 induction, and learn when a high score is a reason… Ragini Mishra 15 min read Molecular Modeling How to Write a Molecular Docking and MD Results Section Report docking and MD results the way examiners expect: the affinity table, the redocking control, which plots earn a figure, and standalone… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Dock a Ligand to DNA or RNA (rDock and Vina) Dock a small molecule to a DNA duplex or an RNA riboswitch: receptor prep, box placement, real rDock commands, and when Vina… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling PyMOL Commands for Docking and MD: Beginner Cheat Sheet Learn the PyMOL commands docking and MD students use every week, from binding-site selections to polar contacts and ray-traced figures. Start here. Dr. Abdul Rajjak Shaikh 12 min read
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