Fast and accurate protein structure search with Foldseek
Michel van Kempen, Stephanie Kim, Charlotte Tumescheit, Milot Mirdita, Jeong-Jae Lee, Cameron L. M. Gilchrist, Johannes Söding, Martin Steinegger
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.
Topics & Concepts
BottleneckAlphabetComputer scienceComputationProtein structureProtein tertiary structureComputational biologyInformation retrievalAlgorithmChemistryBiologyBiochemistryLinguisticsPhilosophyEmbedded systemProtein Structure and DynamicsMachine Learning in BioinformaticsRNA and protein synthesis mechanisms