Open-ComBind: harnessing unlabeled data for improved binding pose prediction.

ABSTRACT: Determination of the bound pose of a ligand is a critical first step in many in silico drug discovery tasks. Molecular docking is the main tool for the prediction of non-covalent binding of a protein and ligand system. Molecular docking pipelines often only utilize the information of one ligand binding to the protein despite the commonly held hypothesis that different ligands share binding interactions when bound to the same receptor. Here we describe Open-ComBind, an easy-to-use, open-source version of the ComBind molecular docking pipeline that leverages information from multiple ligands without known bound structures to enhance pose selection. We first create distributions of feature similarities between ligand pose pairs, comparing near-native poses with all sampled docked poses. These

SUBMITTER: McNutt AT 

PROVIDER: S-EPMC10703974 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature