Structural Bioinformatics

Learn to superimpose two proteins in PyMOL with align, super and cealign, read the RMSD, pick the right command, and fix zero-atom errors.

Pick a defensible protein target and ligand set before you open AutoDock Vina. Follow the step-by-step selection checklist that survives a viva.

Turn a docked pose into a figure your supervisor accepts. Real PyMOL commands for cartoon-plus-sticks, labelled H-bonds, and a 300 dpi ray-traced render.

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.

Learn to clean a raw PDB for MD: rebuild missing loops, add hydrogens, and fix His, Asp and Cys protonation so your simulation does not crash.

Validate your AlphaFold or homology model with a Ramachandran plot and MolProbity before you waste compute on docking. Learn every score and threshold.

Build a 3D protein model from sequence with SWISS-MODEL, no install. Learn to pick a template and read GMQE and QMEANDisCo before you dock.

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.