Protein Structure
UCSF ChimeraX Tutorial for Beginners: Load, Inspect and Clean a Protein Structure
Learn UCSF ChimeraX in one sitting: fetch a PDB entry, master the 12 core commands, then clean the structure for docking or MD. Start the walkthrough.
How to Predict the Effect of a Mutation on Protein Stability (DynaMut2, mCSM and DDMut): A Step-by-Step Guide
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.
How to Make a Point Mutation in a Protein Structure and Compare It with the Wild Type (PyMOL Mutagenesis + GROMACS)
Mutate a residue in PyMOL, save the mutant correctly, then run a fair wild-type vs mutant MD comparison in GROMACS without overclaiming the result.
How to Download a Protein Structure from the RCSB PDB and Read the File
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.
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.