TM-Align 3D

🔗 Launch Notebook

Overview

This notebook has two primary functionalities:

1. Structure Alignment and Comparison — Calculate TM-score and RMSD between two protein structures using ProDy and tmtools.
2. 3D Visualization — Display aligned structures interactively with py3Dmol, using biopython for file handling and sequence parsing.

Our workflow guides users through three stages:

• loading or fetching structures,
• computing TM-score and RMSD for quantitative comparison, and
• visualizing structural overlap in 3D.

We demonstrate the notebook with examples comparing the Human apo ferritin and a Bullfrog M ferritin to illustrate how TM-score and RMSD reflect global and local similarity between protein folds.

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Metrics Explained

TM-score

• A length-independent metric that measures the topological similarity between two protein structures.

• Introduced by Yang Zhang & Jeffrey Skolnick (2005).
  "TM-align: a protein structure alignment algorithm based on the TM-score."
  Nucleic Acids Research, 33(7), 2302–2309.

• Interpretation:

  • TM-score > 0.75 → Indicates strong similarity
  • TM-score > 0.5 → Generally indicates similar folds.
  • TM-score < 0.3 → Typically indicates unrelated structures.
  

RMSD (Root Mean Square Deviation)

• Measures the average atomic deviation between equivalent atoms after optimal superposition.
• Lower RMSD values indicate higher structural similarity.
• Sensitive to local deviations, while TM-score captures global fold similarity.

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Features

• Compare any two PDB structures.
• Compute TM-score and RMSD in seconds.
• 3D visualization of aligned structures using interactive molecular viewers (e.g., py3Dmol.
• Compare & visualize in monomer and multimer mode.
• Sequence alignment.
• Easy to test your own generated structures.

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