Protein Test Set and Receptor Grid Generation Input Files

This directory contains protein structure and model files, and receptor grid generation input files. The files are organized into several subdirectories as follows: ORIGINAL TEST SET: - fragment_bound_xray_structures/: contains 33 .pdb files corresponding to experimentally determined x-ray protein crystal structures with bound fragments. File names begin with UniProt IDs of corresponding proteins (e.g. B9MKT4_frag_bound_protein.pdb) - larger_ligand_bound_xray_structures/: contains 33 .pdb files corresponding to experimentally determined x-ray protein crystal structures with bound larger ligands. File names begin with UniProt IDs of corresponding proteins (e.g. B9MKT4_larger_ligand_bound_protein.pdb) - AF_models/: contains 33 .pdb files corresponding to AF2-generated protein models downloaded from EMBL-EBI database. File names begin with UniProt IDs of corresponding proteins (e.g. B9MKT4_AF.pdb) - AF_ensembles/: contains 33 folders corresponding to each protein in the test set. Each folder contains an ensemble of 500 AF2-generated protein models. The models are named with respect to rank (1-500), model (1-5), and seed (0-99) of the generated model (e.g. rank_001_model_2_seed_088) - receptor_grid_input_files/: contains 2 folders for_AF_models/ and for_unbound_structures/. Each folder contains input files for receptor grid generation when using a probe from FTMap consensus site to define the box center for AF models and unbound structures, respectively (these center coordinates are for box configurations 2 and 3). The coordinates of the box center are in-line with GRID_CENTER. PLINDER TEST SET: -plinder_AF_ensembles/: contains 32 folders corresponding to each protein from the PLINDER-curated set. Each folder contains an ensemble of 500 AF2-generated protein models. The models are named with respect to rank (1-500), model (1-5), and seed (0-99) of the generated model (e.g. rank_001_model_2_seed_088) -plinder_AF_models/: contains 32 .pdb files corresponding to AF2-generated protein models in the PLINDER-curated set, downloaded from EMBL-EBI data. Instances for which no AF2 model was found in the database, the model with highest pLDDT from the AF2 ensemble (rank001) was used. -plinder_ligand_bound_xray_structures/: contains 32 .pdb files correspodning to expreimentally determined X-ray protein crystal structures in the PLINDER-curated set. -plinder_receptor_grid_input_files/: contains input files for receptor grid generation when using a probe from FTMap consensus site to define the box center docking to protein structures and models in the PLINDER-curated set.