datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
PDB
PDB mmCIF Entry Index
The Protein Data Bank is the single global archive of experimentally-determined 3D structures of biological macromolecules, established in 1971 and now holding well over 230,000 entries. It stores atomic coordinates for proteins, nucleic acids, and their complexes determined by X-ray crystallography, cryo-EM, NMR, micro-electron diffraction, and integrative methods, along with the underlying experimental data (structure factors, EM maps, NMR restraints) and… See the full description on the dataset page: https://huggingface.co/datasets/LiteFold/PDB.pdb-dbCDDB-PDB-Protein-50-512
CDDB–PDB Protein Structures, 50–512 Residues
Curated sequences, observed atomic coordinates, physical side-chain torsions,
observation masks, and separately filtered intrinsic-backbone labels for protein
generation and conditional modeling.
Training PDB cutoff: 31 December 2023, inclusive, using the entry's
initial public release date. The source snapshot was collected on
11 September 2026. These dates serve different purposes: historical entries use
their audited coordinates… See the full description on the dataset page: https://huggingface.co/datasets/alegendaryfish/CDDB-PDB-Protein-50-512.PDB-Monomeric-Structure-ESMFold2
PDB-Monomeric-Structure-ESMFold2
Monomeric, protein-only PDB structure dataset for minimum ESMFold2-style
training. Each row is one eligible single-chain biological assembly with a
canonical amino-acid sequence input and all-atom protein labels in atom37.
Labels
atom37_positions: residue x 37 x 3 coordinates, with zeros for missing atoms.
atom37_mask: residue x 37 resolved-atom mask.
aatype, residue_index, auth_seq_id, insertion_code, residue_name, ca_mask.… See the full description on the dataset page: https://huggingface.co/datasets/Synthyra/PDB-Monomeric-Structure-ESMFold2.pdbbind_affinitiespdb_swissprotPDB-Chain-Complex-Benchmark-Rigor
PDB-Chain-Complex-Benchmark-Rigor
Rigor rebuild of Synthyra/PDB-Chain-Complex-Benchmark with split assignments
recomputed from the published chain and complex parquet artifacts.
Split Policy
Splits are assigned by connected components over exact sequence, sequence hash,
30% sequence cluster, structure cluster, source split component, same-PDB
asymmetric-unit membership, chain assembly membership, and biological assembly
co-membership from the complex rows. The… See the full description on the dataset page: https://huggingface.co/datasets/Synthyra/PDB-Chain-Complex-Benchmark-Rigor.pdbbind_refinedPDB-Single-Hard
PDB-Single-Hard: Precise Debugging Benchmarking — hard single-line bug subset
📄 Paper ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Single-Hard is the hard single-line bug subset of the PDB (Precise Debugging Benchmarking) evaluation suite. Every example pairs a ground-truth program with a synthesized buggy version plus a line-level edit script (gt_diff) that encodes the minimal correct fix.
Source datasets: BigCodeBench + LiveCodeBench
Sibling datasets: PDB-Single ·… See the full description on the dataset page: https://huggingface.co/datasets/Precise-Debugging-Benchmarking/PDB-Single-Hard.PDB-Single
PDB-Single: Precise Debugging Benchmarking — single-line bug subset
📄 Paper ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Single is the single-line bug subset of the PDB (Precise Debugging Benchmarking) evaluation suite. Every example pairs a ground-truth program with a synthesized buggy version plus a line-level edit script (gt_diff) that encodes the minimal correct fix.
Source datasets: BigCodeBench + LiveCodeBench
Sibling datasets: PDB-Single-Hard · PDB-Multi… See the full description on the dataset page: https://huggingface.co/datasets/Precise-Debugging-Benchmarking/PDB-Single.PDB-Chain-Complex-Benchmark
PDB-Chain-Complex-Benchmark
PDB-derived protein chain and biological assembly benchmark with strict
sequence, sequence-cluster, structure-cluster, and component-disjoint splits.
Configs
chains: one row per protein polymer chain instance.
complexes: one row per biological assembly with list-valued member chains.
Split Policy
Rows are split by connected components over exact sequence duplicate groups,
30% MMseqs2 sequence clusters, Foldseek… See the full description on the dataset page: https://huggingface.co/datasets/Synthyra/PDB-Chain-Complex-Benchmark.protein_chain_conformational_states
Schema description:
The manually curated dataset of open-closed monomers is included here as benchmarking_monomeric_open_closed_conformers.csv.
Column descriptions:
Schema description:
The manually curated dataset of open-closed monomers is included here as benchmarking_monomeric_open_closed_conformers.csv.
Column descriptions:
UNP_ACC | UniProt accession code
UNP_START | Start of UniProt sequence for given PDBe entries
UNP_END | End of UniProt sequence for given… See the full description on the dataset page: https://huggingface.co/datasets/PDBEurope/protein_chain_conformational_states.PDB-Multi
PDB-Multi: Precise Debugging Benchmarking — multi-line bug subset (2–4 line blocks)
📄 Paper ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Multi is the multi-line bug subset (2–4 line blocks) of the PDB (Precise Debugging Benchmarking) evaluation suite. Every example pairs a ground-truth program with a synthesized buggy version plus a line-level edit script (gt_diff) that encodes the minimal correct fix.
Source datasets: BigCodeBench + LiveCodeBench
Sibling datasets:… See the full description on the dataset page: https://huggingface.co/datasets/Precise-Debugging-Benchmarking/PDB-Multi.protein_secondary_structure_from_PDBThis dataset contains 125,955 protein sequences, with protein PDB ID, length, the sequence (primary structure), as well as secondary structure as identified from experiment. The shortest protein is composed of only 11 amino acids, along with the longest one that features up to 19,350 amino acids. The standard deviation of the length is 855 amino acids.
The dataset further includes overall secondary sturctrure content, for all eight classes of secondary structure types.
The beta sheet content… See the full description on the dataset page: https://huggingface.co/datasets/lamm-mit/protein_secondary_structure_from_PDB.PDB-CCD
PDB Chemical Component Dictionary
PDB-CCD is the Chemical Component Dictionary used by the Protein Data Bank to describe residues, modified residues, ligands, solvents, and other chemical components in macromolecular structures.
Splits
The split is deterministic by component identifier: sha256(component_id) % 10. Bucket 0 is test; buckets 1 through 9 are train.
Split
Rows
train
45,045
test
5,009
total
50,054
Dataset Statistics… See the full description on the dataset page: https://huggingface.co/datasets/LiteFold/PDB-CCD.ecoli_pdb_benchmark_colocalized2022-12-17-pdb-intersect-pisces_pc30_r2.5pdbooks_testPDB-Wild
PDB-Wild: multi-line and real-world repo bug subset
📄 Paper (coming soon) ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Wild is the multi-line and real-world repo bug subset of the PDB (Precise Debugging Benchmarking)
evaluation suite. Every example pairs a ground-truth program with a synthesized
buggy version plus a line-level edit script (gt_diff) that encodes the
minimal correct fix.
Anonymous release for NeurIPS 2026 Datasets & Benchmarks review.
Statistics… See the full description on the dataset page: https://huggingface.co/datasets/anon-pdb/PDB-Wild.keratin-pdb
Human Keratin AlphaFold PDB Structures
Curated human keratin AlphaFold PDB structure records with source metadata, raw PDB text, chain/residue/atom summaries, and pLDDT confidence statistics parsed from the B-factor column.
Keratin Protein Background and Study Significance
Keratins are structural proteins that form intermediate filaments in epithelial tissues, including hair, skin, and nails. In hair fibers, keratin proteins assemble into hierarchical structures… See the full description on the dataset page: https://huggingface.co/datasets/lamm-mit/keratin-pdb.2022-12-17-pdb-intersect-pisces_pc30_r2.5_processed_1024_ankh_testPDB-Single
PDB-Single: single-line bug subset
📄 Paper (coming soon) ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Single is the single-line bug subset of the PDB (Precise Debugging Benchmarking)
evaluation suite. Every example pairs a ground-truth program with a synthesized
buggy version plus a line-level edit script (gt_diff) that encodes the
minimal correct fix.
Anonymous release for NeurIPS 2026 Datasets & Benchmarks review.
Statistics
Total examples: 5751
Per… See the full description on the dataset page: https://huggingface.co/datasets/anon-pdb/PDB-Single.pdb_protein_dataset_100_4000_1024PDB Sequence data with filters for proteins and length.
Min length: 100
Max length: 4000
Context Window: 1024
Any sequence greater than 1024 is split into
multiple smaller sequences of the context length.
pdbbind_refined_with_graph_dictmirror-PDB-Single-Hard
PDB-Single-Hard: Precise Debugging Benchmarking — hard single-line bug subset
📄 Paper ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Single-Hard is the hard single-line bug subset of the PDB (Precise Debugging Benchmarking) evaluation suite. Every example pairs a ground-truth program with a synthesized buggy version plus a line-level edit script (gt_diff) that encodes the minimal correct fix.
Source datasets: BigCodeBench + LiveCodeBench… See the full description on the dataset page: https://huggingface.co/datasets/alucent/mirror-PDB-Single-Hard.mirror-PDB-Single
PDB-Single: Precise Debugging Benchmarking — single-line bug subset
📄 Paper ·
💻 Code ·
🌐 Project page ·
🏆 Leaderboard
PDB-Single is the single-line bug subset of the PDB (Precise Debugging Benchmarking) evaluation suite. Every example pairs a ground-truth program with a synthesized buggy version plus a line-level edit script (gt_diff) that encodes the minimal correct fix.
Source datasets: BigCodeBench + LiveCodeBench
Sibling datasets:… See the full description on the dataset page: https://huggingface.co/datasets/alucent/mirror-PDB-Single.pdb_1000_pairpdb_100_pair