AlphaFold
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 errors.
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 and fit.
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 threshold.
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 the model is good enough to dock.