DOCKING

LightDock

From the GitHub repository: LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm. The LightDock framework is highly versatile, with many options that can be further developed and optimized by the users: it can accept any user-defined scoring function, can use local gradient-free minimization, the simulation can be restrained from the beginning to focus on user-assigned interacting regions, it supports residue restraints in both receptor and ligand partners.

More information is available on the LightDock website. References are listed on the Help page.

SCORING

DockScore 2.0

Our scoring function, DockScore 2.0 (DS2), uses physico-chemical interface features and machine learning to distinguish native-like poses from decoys. The features are first computed using a Python re-implementation of the scoring function from the DOCKSCORE paper. The features are then passed through an XGBoost filter that distinguishes between incorrect and correct (acceptable, medium and high quality - based on CAPRI criteria) poses. The correct poses are then ranked using a graph neural network.

This pipeline has been trained, validated and tested on the BM5.5 dataset with complexes generated using LightDock. Additionally, out-of-distribution performance has been evaluated on the CAPRI Scoreset v2022.

The source code is available on GitHub.

INTERFACE ASSESSMENTt

PPCheck

From the webserver: PPCheck is a webserver that can be used to measure the strength of interactions between any two given proteins/chains, provided their coordinates are available in a single PDB file. The interactions are measured using standard energy calculations involving non-bonded interactions like van der Waals, electrostatic and hydrogen bonds. The sum of these interactions is expressed as pseudoenergy, whose ranges have been standardized using known sets of protein-protein complexes. All the residues which individually participate in any of these interactions are considered to be present at the interface and are listed. The PPCheck webserver can also be used to find 'hotspots' at the interface.

More information is available on the PPCheck website. References are listed on the Help page.