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Protein Test Set and Receptor Grid Generation Input Files

Name: Protein Test Set and Receptor Grid Generation Input Files
Published: 2026-04-06
License: cc-by-4.0

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 co

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CreatorMaidanik, Hlib

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Published2026-04-06

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DOI10.5281/zenodo.19440278

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Downloads106

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Licensecc-by-4.0

File Size679.4 MB

Data TypeDataset

Published2026

Licensecc-by-4.0

Total Views85

Total Downloads106

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 b

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Protein Test Set and Receptor Grid Generation Input… (Full Dataset)679.4 MB

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ReadmeVia DOI record

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Files are hosted on the source repository. Click download to access the full dataset.

Maidanik, Hlib (2026). Protein Test Set and Receptor Grid Generation Input Files. https://doi.org/10.5281/zenodo.19440278

Protein Test Set and Receptor Grid Generation Input Files

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