Fast and accurate protein structure search with Foldseek
By Michel van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, J. Lee, Cameron L. M. Gilchrist, Johannes Söding, Martin Steinegger. bioRxiv, 2022
2,036 citations recorded by the source corpus.
Foldseek speeds up protein structural search by four to five orders of magnitude. As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek aligns the structure of a query protein against a database by describing tertiary amino acid interactions within proteins as sequences over a structural alphabet. Foldseek decreases computation times by four to five orders of magnitude with 86%, 88% and 133% of the sensitivities of Dali, TM-align and CE, respectively.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/655fa18c26267f33084647b30fb0964ec199cd97
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Citations in the corpus
- Clustering predicted structures at the scale of the known protein universe (2023, methodology): “After this step, the structures that have been assigned already are removed from the set and the remaining representative member hits are aligned using Foldseek’s structural Gotoh–Smith–Waterman algorithm 15 , and all passing hits are clustered as well.”
- SaProt: Protein Language Modeling with Structure-aware Vocabulary (2024, methodology): “Here, we simply utilize Foldseek (van Kempen et al., 2023), a purpose-built tool.”
- Empowering Biomedical Discovery with AI Agents (2024, positive): “FoldSeek [42] retrieves protein structures from the AlphaFold DB by translating query structures into 3D interaction alphabet sequences and using pretrained substitution matrices.”