Fig. 1: Foldseek-Multimer schematic.
From: Rapid and sensitive protein complex alignment with Foldseek-Multimer
a, Foldseek-Multimer allows fast querying of input complex(es) against a large database, potentially containing millions of targets. b, All chains from the query (gray) are compared to those of each target (red). A prefilter allows to quickly reject non-matching chain pairs so the full alignment is only applied to promising complex pairs. c, Foldseek-Multimer represents each chain-to-chain alignment as a superposition, described by rotations and translations, required for superposing the target chain onto the query. In this simplified example, two chain-to-chain alignments (top, bottom) are a rotation along one axis (yellow and green highlights), while one (middle) is a rotation along a different axis. d, The complex-to-complex alignment is inferred from chain-to-chain alignments as the superpositions of chain pairs in the complex alignment are similar (‘Algorithm: overview’). Foldseek-Multimer uses the DBSCAN algorithm iteratively, with increasing radii, to identify superposition clusters and the best-scoring valid cluster for computing the complex alignment (Supplementary Fig. 1). e, Based on the best-scoring cluster, the complex TM score is computed across all chain alignments between query and target.
