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• W4386708656 abstract "Abstract Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy 1 , and over 214 million predicted structures are available in the AlphaFold database 2 . However, studying protein structures at this scale requires highly efficient methods. Here, we developed a structural-alignment-based clustering algorithm—Foldseek cluster—that can cluster hundreds of millions of structures. Using this method, we have clustered all of the structures in the AlphaFold database, identifying 2.30 million non-singleton structural clusters, of which 31% lack annotations representing probable previously undescribed structures. Clusters without annotation tend to have few representatives covering only 4% of all proteins in the AlphaFold database. Evolutionary analysis suggests that most clusters are ancient in origin but 4% seem to be species specific, representing lower-quality predictions or examples of de novo gene birth. We also show how structural comparisons can be used to predict domain families and their relationships, identifying examples of remote structural similarity. On the basis of these analyses, we identify several examples of human immune-related proteins with putative remote homology in prokaryotic species, illustrating the value of this resource for studying protein function and evolution across the tree of life." @default.
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• W4386708656 date "2023-09-13" @default.
• W4386708656 modified "2023-10-12" @default.
• W4386708656 title "Clustering-predicted structures at the scale of the known protein universe" @default.
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• W4386708656 doi "https://doi.org/10.1038/s41586-023-06510-w" @default.
• W4386708656 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37704730" @default.
• W4386708656 hasPublicationYear "2023" @default.
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