Python for Structural Biology Cheat Sheet: BioPython and MDAnalysis Essential Commands Quick reference — all levels Every essential command for BioPython and MDAnalysis — organized by task, not alphabetically. Bookmark this and keep it open while you code. Jump to section Environment setup BioPython — loading structures BioPython — navigation and access BioPython — calculations…
Common BioPython and MDAnalysis Mistakes and How to Fix Them 12 min read All levels Most BioPython and MDAnalysis errors are silent — the code runs without crashing but produces wrong residue counts, inflated RMSD values, or empty selections. These are the eight mistakes that appear most often in help threads, and the fixes that…
How to Parse AutoDock Vina Docking Results with Python: From PDBQT to Ranked Hit List 11 min read Intermediate — basic Python and pandas assumed A virtual screening run produces hundreds or thousands of PDBQT output files. Manually opening each one to copy binding affinities is impractical from the first compound. This tutorial builds a…
How to Automate GROMACS Analysis with Python: RMSD, RMSF and Energy Plots 12 min read Intermediate — basic Python and GROMACS assumed Every GROMACS analysis workflow involves the same sequence of terminal commands, interactive group selections, and XVG file parsing repeated across every simulation. Python’s subprocess module automates all of it — this tutorial builds…
How to Analyze Protein-Ligand Interactions over an MD Trajectory with MDAnalysis 11 min read Intermediate — basic MDAnalysis assumed Running a protein-ligand MD simulation is only half the work. The analysis — does the ligand stay in the pocket? Which contacts persist? Which key distances are maintained? — is what produces the data that goes…
How to Analyze Hydrogen Bonds in MD Simulations with MDAnalysis 11 min read Intermediate — basic MDAnalysis assumed H-bond analysis answers the questions that RMSD can’t: which specific interactions stabilize the protein fold? Which residues form persistent contacts with the ligand? MDAnalysis’s HydrogenBondAnalysis class finds every H-bond in every frame automatically — this tutorial shows…
How to Calculate RMSD and RMSF from MD Simulations with MDAnalysis 12 min read Intermediate — basic MDAnalysis assumed RMSD and RMSF are the two most reported metrics from MD simulations — the first tells you whether the simulation is stable, the second tells you which parts of the protein are flexible. This tutorial covers…
MDAnalysis Tutorial for Beginners: Loading and Working with MD Trajectories in Python 12 min read Beginner — basic Python assumed MDAnalysis turns a molecular dynamics trajectory — which is just a large binary file — into a Python object you can slice, select, iterate, and compute with. This tutorial covers the essentials: loading your simulation,…
How to Find and Analyze Protein-Protein Interfaces with BioPython 11 min read Intermediate — basic BioPython assumed Protein-protein interfaces determine binding specificity, drug targetability, and the functional logic of multi-subunit complexes. BioPython’s NeighborSearch class finds interface residues in milliseconds — and from there you can extract contact pairs, compute buried surface area, and produce a…
How to Calculate RMSD and Align Protein Structures with Python and BioPython 11 min read Intermediate — basic BioPython assumed RMSD is the standard metric for quantifying how similar two protein structures are. BioPython’s Superimposer class calculates it in three lines — but the lines before those three, where you select the right atoms to…