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Fast and accurate protein structure search with Foldseek
Michel van Kempen (Max Planck Institute for Multidisciplinary Sciences), Stephanie S. Kim (Seoul National University), Charlotte Tumescheit (Seoul National University), Milot Mirdita (Seoul National University, Max Planck Institute for Multidisciplinary Sciences), Jeong-Jae Lee (Seoul National University), Cameron L. M. Gilchrist (Seoul National University), Johannes Söding (Max Planck Institute for Multidisciplinary Sciences, Campus-Institut Data Science (CIDAS)), Martin Steinegger (Seoul National University)
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.