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Updated: Oct 16, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
LoL-align: sensitive and fast probabilistic protein structure alignment
Lasse Reifenrath1, Michel van Kempen1, Gyuri Kim2,3
1Quantitative and Computational Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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 Cα - Cα 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.
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