About LightDock

LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.

The framework is written in the Python programming language (version >3.5) and allows the users to incorporate their own scoring function.

The LightDock framework is highly versatile, with many options that can be further developed and optimized by the users:

  • Accepts any user-defined scoring function.
  • Backbone flexibility can enabled/disabled for receptor and ligand molecules in an independent way.
  • Can use local gradient-free minimization.
  • The simulation can be restrained from the beginning to focus on user-assigned interacting regions, for example, transmembrane domains or highly-variable loops in antibody-antigen systems.
  • Residue restraints in both receptor and ligand partners.
  • Support for the use of pre-calculated conformers for both receptor and ligand.
  • Support for explicit membrane docking (experimental).

Help and new features request

LightDock is in continuous development and improvement. If you experience any problem with the software, a new feature in mind or you want to collaborate, you have multiple options:

  1. Open a new issue in the LightDock main repository
  2. Or write an email to b.jimenezgarcia@uu.nl

License

LightDock is available under GPLv3 License. If you have any doubt, please don’t hesitate to contact us at b.jimenezgarcia@uu.nl.