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004248f5ea6ec37d88e8b5ce337488d6 | 84 | [
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End of preview. Expand in Data Studio
OpenFold3 structures for Rfam seed alignments
OpenFold3 structures, MSAs and RNAView base pairs for every unique sequence in the Rfam 15.1 seed alignments.
- Sequences: Rfam 15.1 seed alignments (
Rfam.seed.gz), 98,542 unique sequences. - MSAs: nhmmer against OpenFold3's RNA databases, keeping the 10,000 best hits per database:
- Rfam 14.9 (
rfam.fasta.gz) - RNAcentral 21.0 (
rnacentral.fasta.gz) - NCBI Nucleotide collection, February 2024 snapshot (
nucleotide_collection.fasta.gz)
- Rfam 14.9 (
- Model: OpenFold3 v0.5.0, checkpoint
of3-ob-2025-06-30-174k.pt.num_diffusion_samples=5,seeds=[0]for 98,272 unique sequences (>2,852 nt OOM on H200).
Data for Narrowing the RNA sequence-structure gap: OpenFold3 models for all Rfam RNA structural families (coming soon).
Contents
metadata/sequences.parquet # per sequence: length, families (family, seed_name), state, sample confidences
metadata/members.parquet # per tar member: id, seed, sample, kind, db, shard, offset, size, sha256
pred/<g>.tar # <id>.seed<s>_sample<k>.{model.cif.gz,confidences_aggregated.json,confidences.npz}
msa/<g>.tar # <id>.{rfam,rnacentral,nucleotide_collection}_hits.a3m.gz
bp/<g>.tar # <id>.seed<s>_sample<k>.bp.json
id is the sequence md5, as in Rfam's seed_region table; g is id[:2]. Tars are uncompressed, so a single member can be read by range request from its offset and size.
Citation
Coming soon.
Please also cite:
- Rfam: Rfam 15: RNA families database in 2025 (Nucleic Acids Research, 2025)
- OpenFold3: OpenFold3-preview v0.5.0 (Zenodo, 2026)
- AlphaFold3: Accurate structure prediction of biomolecular interactions with AlphaFold 3 (Nature, 2024)
- RNAView: Tools for the automatic identification and classification of RNA base pairs (Nucleic Acids Research, 2003)
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