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 >=3.6) and Rust (2021 edition) for selected high computation-intensive parts of the framework.

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, including custom ones.
  • Backbone flexibility can be 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.
  • Integrative approaches such as membrane docking using coarse-grained information.
  • Protein-protein, protein-peptide and protein-DNA support.
  • Shared-memory (multiprocessing) and distributed-memory (MPI).
  • Simulation step is embarrassingly parallel by design and scales very well to the number of CPU cores in HPC architectures.

License

LightDock is available under GPLv3 License. If you have any doubt, please don’t hesitate to contact us at lightdocking@gmail.com.

With the support of:




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