Dali server: structural unification of protein families

Abstract Protein structure is key to understanding biological function. Structure comparison deciphers deep phylogenies, providing insight into functional conservation and functional shifts during evolution. Until recently, structural coverage of the protein universe was limited by the cost and labo...

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Bibliographic Details
Published in:Nucleic acids research 2022-07, Vol.50 (W1), p.W210-W215
Main Author: Holm, Liisa
Format: Article
Language:English
Subjects:
Computers
Databases, Protein
Internet
Protein Conformation
Proteins - chemistry
Software
Web Server Issue
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Summary:Abstract Protein structure is key to understanding biological function. Structure comparison deciphers deep phylogenies, providing insight into functional conservation and functional shifts during evolution. Until recently, structural coverage of the protein universe was limited by the cost and labour involved in experimental structure determination. Recent breakthroughs in deep learning revolutionized structural bioinformatics by providing accurate structural models of numerous protein families for which no structural information existed. The Dali server for 3D protein structure comparison is widely used by crystallographers to relate new structures to pre-existing ones. Here, we report two most recent upgrades to the web server: (i) the foldomes of key organisms in the AlphaFold Database (version 1) are searchable by Dali, (ii) structural alignments are annotated with protein families. Using these new features, we discovered a novel functionally diverse subgroup within the WRKY/GCM1 clan. This was accomplished by linking the structurally characterized SWI/SNF and NAM families as well as the structural models of the CG-1 family and uncharacterized proteins to the structure of Gti1/Pac2, a previously known member of the WRKY/GCM1 clan. The Dali server is available at http://ekhidna2.biocenter.helsinki.fi/dali. This website is free and open to all users and there is no login requirement. Graphical Abstract Graphical Abstract Dali server supports structural searches against the Protein Data Bank and AlphaFold Database and annotates structural alignments with Pfam graphics.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkac387