Fast and accurate protein structure search with Foldseek
Michel Kempen, Stephanie S. Kim, Charlotte Tumescheit, and 5 more authors
Nature Biotechnology, 2024
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.