ArticleiScience2022
A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- ATAD3 megadalton complex in Plasmodium falciparum is essential for mitochondrial and cellular viability.PLoS pathogens · 2026Article
- A sponge homolog of BRMS1 reveals ancient origin of metastasis-suppressing functions.BMC biology · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation.Bioinformatics (Oxford, England) · 2025Article
- RNA sculpting by the primordial Helix-clasp-Helix-Strand-Loop (HcH-SL) motif enforces chemical recognition enabling diverse KH domain functions.The Journal of biological chemistry · 2025Review
- Predicted structural proteome of Sphagnum divinum and proteome-scale annotation.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
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Abstract
Many distantly related structure pairs exhibit structural similarities that can only be fully captured by a non-sequential alignment program. We present US-align2, a unified protocol for both sequential and non-sequential alignment of proteins and nucleic acids. On manually curated reference alignments for protein structural pairs with non-sequential relations, US-align2 achieves ≥13% higher agreement with reference alignments than existing sequential and non-sequential alignment methods. Non-sequential alignments also enabled US-align2 to have higher sensitivities in detecting RNA pairs from the same family with sequence identities <40%, obtaining ≥9% higher area under the receiver operating characteristic curve than third-party programs. The unique ability of US-align2 to parse both proteins and nucleic acids allows the method to detect protein-RNA and protein-DNA mimicries. Additionally, US-align2 performs full and semi-non-sequential alignments with at least 48% and 14% faster speed than existing programs for the same tasks, making it particularly useful for large-scale structural similarity detection.
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Registered trials
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