| name | deepblast |
| description | TM-Vec and DeepBLAST — deep learning for protein remote homology and structural alignment from sequences (predict TM-scores; align homologous regions without solved structures). Use when: (1) Searching structure-like similarity in large sequence DBs, (2) Aligning remote homologs for annotation, (3) Complementing PLMSearch / Foldseek workflows. Upstream: https://github.com/tymor22/tm-vec and https://github.com/flatironinstitute/deepblast. Route via protein-language-model.
|
| license | MIT |
| category | analysis-tools |
| tags | ["DeepBLAST","TM-Vec","remote-homology","structure","PLM"] |
| upstream | https://github.com/flatironinstitute/deepblast |
| stage | function |
TM-Vec / DeepBLAST
Upstream: tm-vec ·
deepblast
Citation
Hamamsy, T. et al. Protein remote homology detection and structural alignment
using deep learning. Nat. Biotechnol. 42, 975–985 (2024).
https://doi.org/10.1038/s41587-023-01917-2
See also docs/references.md.
Analytical thinking
| Component | Role |
|---|
| TM-Vec | Predict structural similarity (TM-score-like) from sequence pairs; search large DBs |
| DeepBLAST | Structurally align proteins from sequence by identifying homologous regions |
Designed for the metagenomic reality that many proteins lack close sequence
neighbors but retain structural homology. Complementary to plmsearch and to
structure search (Foldseek) when structures/pLDDT models exist.
How to run
Decision tree
Remote homology workflow?
├─ Fast PLM embedding search → plmsearch
├─ TM-score search + structural alignment → deepblast (TM-Vec)
├─ Have structures / AFDB → foldseek (± folddisco / spacedust)
└─ Close homologs → mmseqs2 / diamond
Related skills
protein-language-model · esm · plmsearch · metagenomics-llm ·
foldseek · folddisco · spacedust · mmseqs2 · eggnog-mapper ·
tool-selection
