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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 proteins structures, requiring fast and accurate MSTA methods. Here, we introduce FoldMason, a progressive MSTA method that leverages the structural alphabet from Foldseek, a pairwise structural aligner, for multiple alignment of hundreds of thousands of protein structures, exceeding alignment quality of state-of-the-art methods, while two orders of magnitudes faster than other MSTA methods. FoldMason computes confidence scores, offers interactive visualizations, and provides essential speed and accuracy for large-scale protein structure analysis in the era of accurate structure prediction. Using Flaviviridae glycoproteins, we demonstrate how FoldMason’s MSTAs support phylogenetic analysis below the twilight zone. FoldMason is free open-source software:
foldmason.foldseek.com
and webserver:
search.foldseek.com/foldmason
.
Academic Publication Multiple Protein Structure Alignment at Scale with FoldMason
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Multiple Protein Structure Alignment at Scale with FoldMason
Abstract Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computati...
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Abstract Motivation Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioi...
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Abstract Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein struct...
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AbstractThe introduction of AlphaFold 21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and desig...
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets
Abstract Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple g...
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What is the core focus of the research titled 'Multiple Protein Structure Alignment at Scale with FoldMason'?
This literature focuses on: 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 r...
Are there open-source GitHub repositories related to Multiple Protein Structure Alignment at Scale with FoldMason?
Yes, open-source projects like calesthio/Crucix (Your personal intelligence agent. Watches the world from multiple data sources and pings you when something changes.) are actively building upon these concepts.
Which startups are commercializing the technology behind Multiple Protein Structure Alignment at Scale with FoldMason?
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What other academic literature is closely related to 'Multiple Protein Structure Alignment at Scale with FoldMason'?
Yes, highly correlated activity was mapped. An entry titled 'Multiple Protein Structure Alignment at Scale with FoldMason' discusses this: Abstract Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential f...
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GitHubcalesthio/Crucix
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GitHubalvinunreal/awesome-opensource-ai
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Product Huntgigabrainz — Learn Anything, 10x Faster
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