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May 8, 2023Nature Biotechnology2,573 citationsOpen Access

Fast and accurate protein structure search with Foldseek

MKMichel van KempenSKStephanie KimCTCharlotte Tumescheit

Key Points

  • The aim is to enhance protein structure searching efficiency in large databases using Foldseek.
  • Foldseek aligns query protein structures against databases using a structural alphabet.
  • It models tertiary amino acid interactions to describe protein structures.
  • Performance compared to Dali, TM-align, and CE in terms of sensitivity and computation time.
  • Foldseek reduces computation times by four to five orders of magnitude.
  • Achieves 86%, 88%, and 133% sensitivity compared to Dali, TM-align, and CE, respectively.

Abstract

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.

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Cite This Study

Kempen et al. (2023) studied this question.

synapsesocial.com/papers/69d7f7a166a29169b4bed9e7https://doi.org/10.1038/s41587-023-01773-0
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Also Consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

  1. 1Protein structure alignment by incremental combinatorial extension (CE) of the optimal path1998 · 2,097 citations
  2. 2Structure is three to ten times more conserved than sequence—A study of structural response in protein cores2009 · 616 citations
  3. 3Fast procedure for reconstruction of full‐atom protein models from reduced representations2008 · 433 citations
  4. 4HOMSTRAD: A database of protein structure alignments for homologous families1998 · 511 citations
  5. 5lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests2013 · 1,279 citations