Protein structure alignment by Reseek improves sensitivity to remote homologs.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39546374.
- Also identified by DOI 10.1093/bioinformatics/btae687 and PMC identifier 11601161.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Recent breakthroughs in protein fold prediction from amino acid sequences have unleashed a deluge of new structures, presenting new opportunities and challenges to bioinformatics. Reseek is a novel protein structure alignment algorithm based on sequence alignment where each residue in the protein backbone is represented by a letter in a "mega-alphabet" of 85 899 345 920 (∼1011) distinct states. Reseek achieves substantially improved sensitivity to remote homologs compared to state-of-the-art methods including DALI, TMalign, and Foldseek, with comparable speed to Foldseek, the fastest previous method. Scaling to large databases of AI-predicted folds is analyzed. Foldseek E-values are shown to be under-estimated by several orders of magnitude, while Reseek E-values are in good agreement with measured error rates. https://github.com/rcedgar/reseek.
Medical subject headings
- Algorithms
- Proteins
- Sequence Alignment