How to Download and Parse AlphaFold Structures with Python and BioPython 11 min read Intermediate — basic BioPython assumed Every AlphaFold prediction is one API call away. Python makes it trivial to download hundreds of structures, extract their per-residue confidence scores, and filter out unreliable regions — automating what would otherwise be hours of manual…
How to Calculate Protein Properties with BioPython: Molecular Weight, GRAVY and Secondary Structure 11 min read Beginner — basic BioPython assumed BioPython’s ProteinAnalysis class turns any protein sequence into a dashboard of physicochemical properties with a handful of method calls. This tutorial covers every property the class computes, what each value means biologically, and how…
BioPython Tutorial for Beginners: Parsing PDB Files and Working with Protein Structures 12 min read Beginner — basic Python assumed BioPython’s structure module turns a PDB file — which is just a formatted text file — into a Python object you can query, iterate, and calculate with. This tutorial covers everything you need to go…
How to Set Up a Python Environment for Structural Biology (2026) 10 min read Beginner Getting your Python environment right is the unglamorous prerequisite to everything else. Do it once properly — with conda, a dedicated environment, and all the right packages — and you’ll never hit a dependency conflict or a “module not found”…
Python for Structural Biology: The Complete Guide to BioPython and MDAnalysis 30 min read Intermediate Python assumed Python is the language that connects every other tool in structural biology. It parses the PDB files you download, analyzes the trajectories you simulate, filters the docking results you generate, and automates the figure pipelines you build in…