Tutorials
IDP

IDP

Description

This tutorial uses an adaptation of the CALVADOS2 model implemented at DOI: 10.5281/zenodo.13754000 and creates the Spectrum of London Axilrod–Teller–Muto representation (SLATM).

Click directly into Google collab link

Folder Structure

  • Simulation Code: Contains an interactive Google Colab notebook for simulating both single-peptide assembly and co-assembly.
  • SLATM Representation: Includes an interactive notebook for generating SLATM representations.

References

  1. G. Tesei, T. K. Schulze, R. Crehuet, K. Lindorff-Larsen. Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. PNAS (2021), 118(44):e2111696118. DOI: 10.1073/pnas.2111696118
  2. G. Tesei, K. Lindorff-Larsen. Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range. Open Research Europe (2022), 2(94). DOI: 10.12688/openreseurope.14967.2
  3. F. Cao, S. von BĂĽlow, G. Tesei, K. Lindorff-Larsen. A coarse-grained model for disordered and multi-domain proteins. Protein Science (2024), 33(11):e5172. DOI: 10.1002/pro.5172
  4. Bing Huang and O. Anatole Von Lilienfeld. “Quantum machine learning using atom-in- molecule-based fragments selected on the fly”. In: Nature Chemistry 12.10 (Oct. 2020), pp. 945–951.

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