Multiple protein structure alignment at scale with FoldMason
Seoul National University · Korea Basic Science Institute
Abstract
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our repository of available protein structures, requiring fast and accurate MSTA methods. We introduce FoldMason, a progressive MSTA method that leverages the pairwise structural aligners Foldseek and TM-align for the multiple alignment of hundreds of thousands of protein structures, matching or exceeding the alignment quality of state-of-the-art MSTA methods while being two orders of magnitude faster. Using Flaviviridae glycoproteins, we demonstrate that FoldMason’s MSTAs support phylogenetic analysis beyond the…
Citation impact
- FWCI
- 158.87
- Percentile
- 100%
- References
- 88
Authors
3Topics & keywords
- Pairwise comparison
- Matching (statistics)
- Structural alignment
- Protein structure
- Multiple sequence alignment
- Sequence alignment
- Protein structure prediction
- Phylogenetic tree