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@pol-sb pol-sb released this 14 Dec 11:14
· 27 commits to main since this release
v0.1.0
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Info

First release of the idp-simul code written for the project Modelling small-molecule interactions with intrinsically disordered protein condensates in collaboration with the Theoretical and Computational Chemistry group of the Institute of Advanced Chemistry of Catalonia (IQAC – CSIC).

Features

  • Coarse grained Langevin dynamics simulations of IDP systems using OpenMM.

  • Introduction of amino-acid like small-molecules into the system in order to study thermodynamic parameters of the condensate.

  • Initial version of a simulation dataset included.

  • Simple plotting and result analysis scripts.

  • Capable of performing Monte Carlo minimization of several properties:

    • SASA
    • Dispersion
    • Potential energy

  • Lap test by @pol-sb in #1

  • Parser subcommand by @pol-sb in #2

  • New logger system by @pol-sb in #3

  • Merge branch containing duplicate folder fix by @pol-sb in #5

  • Commented functions and changed push notifications service to ntfy.sh by @pol-sb in #6

  • Merge minimize_sasa with main by @pol-sb in #7

Full Changelog: https://github.com/pol-sb/simul-protein-small-molecule/commits/v0.1.0

Next Features

  • An additional mode will be added to allow to remove the added small molecules from already condensed simulations and then resume these simulations.
  • Improved small molecule capabilities will be included
  • More coarse-grained models.

Please report any bugs or features you would like to see in the next release!

Contributors

pol-sb
Assets 2
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