LoL-align: sensitive and fast probabilistic protein structure alignment

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Abstract
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.
Funding Information
  • Deutsche Forschungsgemeinschaft (RTG2984 Evorest)
  • Deutsche Forschungsgemeinschaft (RTG2984 Evorest)
  • Max-Planck-Gesellschaft
  • National Research Foundation of Korea (RS-2020-NR049543)
  • National Research Foundation of Korea (RS-2020-NR049543, RS-2021-NR061659 and RS-2021-NR056571, RS-2024-00396026)
  • National Research Foundation of Korea (RS-2023-00250470)
  • National Research Foundation of Korea (RS-2020-NR049543, RS-2021-NR061659 and RS-2021-NR056571, RS-2024-00396026)
  • Korea Basic Science Institute (C539200)

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