Structural Bioinformatics

Predict how a point mutation changes protein stability with DynaMut2, mCSM and DDMut, and learn to read the ddG sign correctly before you report it.

Dock two proteins in a browser with ClusPro, HDOCK or HADDOCK. Prepare your files, run the job, and learn which model to keep and why.

Find, download, and actually read a protein structure from the RCSB PDB before you dock or run MD. Start your modelling workflow the right way.

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.