Skip to content

About

Tutorial for CALVADOS simulations

Resources

Stars

1 star

Watchers

1 watching

Forks

Latest commit

 

History

53 Commits

Folders and files

NameName
Last commit message
Last commit date
 
 
 
 
 
 

Repository files navigation

Tutorial IDPs SAPs

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).

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 Bülow, 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.

About

Tutorial for CALVADOS simulations

Resources

Stars

1 star

Watchers

1 watching

Forks

Releases

Packages

Contributors

Languages