Structures
tcren_structures
isalgo/tcren_structures
TCR:peptide:MHC structure sets and benchmarks for TCRen2 (structure-based prediction of TCR
recognition). Fetch with tcren / the manuscript scripts/bootstrap_data.py.
Contents rule: structures as .gz/.tar.gz (LFS) and .txt/.md descriptions only —
no notebooks, figures, or analysis tables.
Layout
folder
task
contents
Native2026/, Canonical2026/
derivation / ergodicity
non-redundant TCR:pMHC structures (.gz)
Native2022/… See the full description on the dataset page: https://huggingface.co/datasets/isalgo/tcren_structures.viral-protein-structuresFolded/Extracted structures from PDB, AF2, ESMAtlas, and additional structures folded via AlphaFold2 on the Kempner Institute H100 GPUs.
datasets-nanophotonic-structureskukulu_prepared_antibody-antigen_structures
Kūkulu Training Data - Prepared and Masked PDB Structures of Antibody-Antigen Complexes
This dataset contains cleaned antibody-antigen complex structures for AI model training. This including two versions of various PDBs:
Prepared: Antibody-antigen complex structures prepared for consistency.
Heavy and light antibody chains, trimmed to the Fv portion.
Removed non-antigen chains (heterogens, waters, and protein chains not part of the complex).
Masked: The same as the prepared… See the full description on the dataset page: https://huggingface.co/datasets/silicobio/kukulu_prepared_antibody-antigen_structures.bioreason-pro-structures
🧬 BioReason-ProAdvancing Protein Function Prediction withMultimodal Biological Reasoning
BioReason-Pro Protein Structures
AlphaFold backbone structures for the proteins in the BioReason-Pro training and
evaluation sets. BioReason-Pro feeds these coordinates to its ESM3 encoder alongside
the amino-acid sequence; ESM3 falls back to sequence-only when a structure is absent,
so these are optional — but the released checkpoint was trained with them.
Covers 131… See the full description on the dataset page: https://huggingface.co/datasets/wanglab/bioreason-pro-structures.syngenome-protein-structures
SynGenome predicted protein structures
This repository contains ~3.7 million ESMFold structure predictions for synthetic protein sequences in SynGenome.
The data is divided into tarball shards and a metadata file:
.
├── shard_0.tar
├── shard_1.tar
├── ...
├── shard_36.tar
└── metadata_summary.csv.gz
Each shard_N.tar file contains ~100k gzipped PDB files. When extracted:
tar -xf shard_0.tar
Creates a directory structure:
shard_0/
├──… See the full description on the dataset page: https://huggingface.co/datasets/evo-design/syngenome-protein-structures.