Structure-derived embeddings outperform sequence-derived embeddings on LM-based alignment

Summary

Structure-derived representations (embeddings) outperform sequence-derived representations on protein alignment (1). They also outperform structure tokenization methods such as alignment using Foldseek alphabets.

See also

• PLM-based sequence searches outperform sequence- and matches structure-based search methods

1.

Trinquier J, Petti S, Park S, Herath K, van Kempen M, Feng S, et al. SoftAlign: End-to-end protein structures alignment. openRxiv; 2025. Available from: https://doi.org/10.1101/2025.05.09.653096