0.1.0

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.

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