bioRxivBioinformaticsPreprint
LoL-align: sensitive and fast probabilistic protein structure alignment
Lasse ReifenrathiD, Michel van KempeniD, Gyuri KimiD, Soo Hyun Kim, Mohammadreza Radnezhad, Milot MirditaiD, Martin SteineggeriD, Johannes SödingiD
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 - C distances. LoL-align is markedly more sensitive in detecting remote homologs than TMalign and DALI on single- and multi-domain benchmarks and achieves better alignment quality at 5-20x their speed. LoL-align is fully integrated into Foldseek.
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