LoL-align: sensitive and fast probabilistic protein structure alignment

The ubiquitous availability of protein structures permits replacing sequence alignment with more accurate and sensitive structure alignment algorithms. LoL-align maximizes a local log-odds score for proteins to be homologous, given their intra-protein C α − C α distances. Here we show that LoL-align is markedly more sensitive in detecting remote homologs than TM-align and Dali on single- and multidomain benchmarks and achieves better alignment quality at 5–20 × their speed. LoL-align is fully integrated into Foldseek.