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1,390 claims from 864 papers are on the record. 46 have been checked so far; the other 1,344 have no check with a result yet.

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Status: Unchecked ×Keyword: Foldseek ×Clear all

2 claims from 2 papers

1. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Fast and accurate protein structure search with Foldseek

   van Kempen, Kim, Tumescheit et al. · Nature Biotechnology · 2023

   The paper presents Foldseek, a tool that searches large protein structure databases by turning 3D structure into sequences over a structural alphabet, aiming to remove a growing search bottleneck.

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   1. UncheckedFoldseek searches protein structures four to five orders of magnitude faster than Dali, TM-align and CE, at 86%, 88% and 133% of their sensitivities.“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.”

2. Biochemistry, Genetics and Molecular Biology › Machine Learning in Bioinformatics

   SaProt: Protein Language Modeling with Structure-aware Vocabulary

   Su, Han, Zhou, Shan, Zhou and Yuan · bioRxiv (Cold Spring Harbor Laboratory) · 2023

   The authors build SaProt, a protein language model that combines residue tokens with structure tokens from Foldseek, trained on about 40 million protein sequences and structures.

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   1. UncheckedThe SaProt protein model is reported to beat well-established baseline models across 10 downstream tasks, which the authors take as showing broad applicability.“Through extensive evaluation, our SaProt model surpasses well-established and renowned baselines across 10 significant downstream tasks, demonstrating its exceptional capacity and broad applicability.”