Fast and Accurate Protein Structure Search with Foldseek

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2023 May 8

PMID 37156916

Authors

Michel van Kempen

Stephanie S Kim

Charlotte Tumescheit

Milot Mirdita

Jeongjae Lee

Cameron L M Gilchrist

Johannes Soding

Martin Steinegger

Affiliations

Soon will be listed here.

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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