“Fast and accurate protein structure search with Foldseek” (2023), by Michel van Kempen et al. Genetics and Biochemistry research paper. Original abstract below, unchanged. A free PDF is available.

Fast and accurate protein structure search with Foldseek

Michel van Kempen, Stephanie S. Kim, Charlotte Tumescheit et al. · May 8, 2023 · Genetics and Biochemistry

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.

Free PDF DOI: 10.1038/s41587-023-01773-0