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TSR Research Group

BioTSR

Learn BioTSR

Learn how TSR represents protein structures and how to use BioTSR through a short video, an interactive example and a hands-on notebook. Start with whichever resource interests you.

1

Watch: How BioTSR works

1 min 25 s · captions · transcript

See how BioTSR encodes triangles of Cα atoms as integer keys and uses shared keys to compare structures.

Read the transcript
  1. 0:00 How BioTSR works. [How BioTSR Works. From a protein structure to structural keys. BioTSR 1.0.0 · TSR Research Group]
  2. 0:04 Ubiquitin: one carbon alpha atom per residue. [Ubiquitin (PDB 1UBQ), chain A: 76 residues, one Cα atom each; real coordinates from PDB entry 1UBQ]
  3. 0:07 Pick three from its hydrophobic patch. [Three Cα atoms of the Ile44 patch: Leu 8, Ile 44, Val 70]
  4. 0:11 Three points, one triangle, one number. [Three points make a triangle; TSR encodes it as one integer, its key]
  5. 0:15 Each residue type has a fixed code. [Each residue type has a code: Val 20, Ile 10, Leu 8]
  6. 0:19 Its shape gives two bins: angle and distance. [Shape: one angle and the longest edge, each sorted into a numbered bin]
  7. 0:23 Codes and bins make one key. [Codes and bins combine into one integer: key 17,637,781]
  8. 0:27 The key records only residue types and shape bins, so different triangles can share it. [Four different triangles in ubiquitin share this key: Val 70 · Ile 44 · Leu 8, Val 5 · Ile 61 · Leu 56, Val 17 · Ile 61 · Leu 15 and Val 70 · Ile 36 · Leu 71; .keys frequency 4]
  9. 0:35 Any three carbon alpha atoms form a triangle: 70,300 in all. [Every set of three Cα atoms is a triangle: 76 atoms give 70,300 triangles]
  10. 0:42 Together, they produce 45,349 distinct keys. [Those 70,300 triangles produce 45,349 distinct keys]
  11. 0:50 Next, barnase, bound to its inhibitor, barstar. [PDB 1BRS: barnase (chain A) bound to its inhibitor barstar (chain D)]
  12. 0:54 The carbon alpha cross method keeps only residues at the interface. [Interface residues have a heavy atom within 8 Å of the other chain (contact cutoff set to 8 Å): 39 in barnase, 35 in barstar]
  13. 0:59 Every cross triangle spans both proteins, like this one. [A cross triangle spans both chains: barnase Arg 59 and His 102, barstar Asp 39; key 19,587,605, one of 49,140 Cα cross triangles, contact cutoff 8 Å]
  14. 1:05 Now compare three samples, each with its own keys. [Three samples: ubiquitin, barnase and barstar, one key set each]
  15. 1:10 9,523 distinct keys occur in all three samples. [9,523 distinct keys occur in all three samples.]
  16. 1:18 BioTSR is open source, from the TSR Research Group. [BioTSR · github.com/TSRMethod/BioTSR · TSR Research Group · tsrmethod.github.io · BioTSR 1.0.0 · Apache License 2.0 (the software licence)]

Download the video (MP4, 21 MB)

Music: “Nebula” by The Grey Room / Density & Time · YouTube Audio Library.

2

Explore: Four triangles, one key

About 5 minutes · in your browser, nothing to install

Four different triangles in ubiquitin have the same key, 17637781. Rotate the real structure, switch between the triangles, and see what a key keeps and what it leaves out.

Open the interactive lesson

Prefer a table? The same four triangles are listed step by step in the worked example on Understand TSR.

3

Run: Your first 10 minutes with BioTSR

About 10 minutes · Jupyter notebook

Install BioTSR, compute every triangle of ubiquitin, find the lesson’s four triangles in BioTSR’s own output, and count the keys that ubiquitin, barnase and barstar share, with a check at every step.

You need Python 3.9–3.13 on Linux or macOS, Jupyter and an internet connection. The notebook writes about 25 MB, all of it into one folder beside it.

Download the notebook (.ipynb) (38 kB)Read the recorded run

The recorded run is the notebook as it ran with BioTSR 1.0.0, outputs included. It is a page to read: nothing runs in your browser.

How to open the notebook
python3 -m venv biotsr-env
source biotsr-env/bin/activate
python -m pip install jupyterlab
jupyter lab biotsr-first-10-minutes.ipynb

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