LeDock

LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows.

The software can run as a standalone programme or from Jupyter Notebook. It supports the Tripos Mol2 file format.

Methodology

LeDock utilizes a simulated annealing and genetic algorithm approach for facilitating the docking process of ligands with protein targets. The software employs a knowledge-based scoring scheme that is derived from extensive prospective virtual screening campaigns. It is categorized as a flexible docking method.

Performance

In a study involving 2,002 protein-ligand complexes, LeDock demonstrated a notable level of accuracy in predicting molecular poses. The Linux version contains command line tools to run automated virtual screening of different large molecular libraries in the cloud.

In a performance evaluation of ten docking programs, LeDock demonstrated strong sampling power when compared against other commercial and academic alternatives. According to a review from 2017, LeDock was noted for its effectiveness in sampling ligand conformational space, identifying near-native binding poses, and having a flexible docking protocol. The Linux version includes tools for high-throughput virtual screening in the cloud.