Tag
AlphaFold
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 Get the Right Protein Sequence from UniProt for Modelling (Canonical Isoform, Signal Peptide and Residue Numbering) Pick a reviewed Swiss-Prot entry, take the canonical isoform, cut the signal peptide, and check the PDB offset before you model. Follow… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling How to Align and Superimpose Two Protein Structures in PyMOL (align, super and cealign): A Step-by-Step Guide Learn to superimpose two proteins in PyMOL with align, super and cealign, read the RMSD, pick the right command, and fix zero-atom… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling AlphaFold vs Homology Modelling vs Experimental Structures: Which to Use, When Learn to choose between an experimental PDB structure, a SWISS-MODEL homology model, or AlphaFold for docking and MD, judged on coverage, confidence… Dr. Abdul Rajjak Shaikh 10 min read Updated Molecular Modeling How to Validate a Protein Structure: Ramachandran Plots and MolProbity Scores Explained Validate your AlphaFold or homology model with a Ramachandran plot and MolProbity before you waste compute on docking. Learn every score and… Dr. Abdul Rajjak Shaikh 10 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