Guild: A flexible end-to-end framework for protein-ligand binding prediction

This dataset accompanies the manuscript “Guild: A flexible end-to-end framework for protein–ligand binding prediction.” It contains the data used to perform large-scale (bulk-mode) protein–ligand binding predictions with DiffDock and AutoDock Vina.

The primary use case focuses on G protein–coupled receptors (GPCRs), including curated combinations of receptor structures with known ligands sourced from the Protein Data Bank (PDB), as well as decoys and experimentally validated binders defined in the manuscript. In addition, the dataset incorporates two broader chemical classes—natural products and synthetic compounds—to support extended benchmarking and generalization analyses.

Overview on data files:

full_combinations_table.csv - CSV with all the combinations of protein-ligand pairs used by the PLBP

pdbs.zip - PDB files for the GPCR proteins used in the case study

gpcrdb_protein_data.csv - Curated metadata on GPCR proteins in the case study

guild_data.zip - Outputs from the PLBP algorithms used in the case study