Tag
Protein Structure Prediction
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 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 Bioinformatics Multi-Epitope Vaccine Structure: Model, Refine, Validate Model a vaccine construct with no template, read the low pLDDT at your linkers correctly, refine it, and validate it before you… Ragini Mishra 13 min read Molecular Modeling MODELLER Tutorial: Build a Homology Model Step by Step Install MODELLER, pick a template, write the align2d alignment, run AutoModel and rank your models by DOPE score, using the official tutorial… Dr. Abdul Rajjak Shaikh 16 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 Molecular Modeling Homology Modelling Tutorial for Beginners: Build a Protein Structure with SWISS-MODEL (Step by Step) Build a 3D protein model from sequence with SWISS-MODEL, no install. Learn to pick a template and read GMQE and QMEANDisCo before… Dr. Abdul Rajjak Shaikh 11 min read Updated Molecular Modeling How to Predict a Protein Structure with AlphaFold (ColabFold, No Install): A Beginner’s Guide Fold your protein sequence with AlphaFold in ColabFold, free and no install. Learn to read pLDDT and PAE so you know if… Dr. Abdul Rajjak Shaikh 11 min read Updated