Dali server : structural unification of protein families

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http://hdl.handle.net/10138/345965

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Holm , L 2022 , ' Dali server : structural unification of protein families ' , Nucleic Acids Research , vol. 50 , no. W1 , pp. W210-W215 . https://doi.org/10.1093/nar/gkac387

Title: Dali server : structural unification of protein families
Author: Holm, Liisa
Contributor organization: University of Helsinki
Organismal and Evolutionary Biology Research Programme
Institute of Biotechnology
Genetics
Bioinformatics
Computational genomics
Date: 2022-07-05
Language: eng
Number of pages: 6
Belongs to series: Nucleic Acids Research
ISSN: 0305-1048
DOI: https://doi.org/10.1093/nar/gkac387
URI: http://hdl.handle.net/10138/345965
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 crystal-lographers 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. [GRAPHICS] .
Subject: TRANSCRIPTION FACTORS
CRYSTAL-STRUCTURE
DNA-BINDING
COMPLEX
LINK
1184 Genetics, developmental biology, physiology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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