ELM-the Eukaryotic Linear Motif resource-2024 update

Manjeet Kumar; Sushama Michael; Jesús Alvarado-Valverde; András Zeke; Tamas Lazar; Juliana Glavina; Eszter Nagy-Kanta; Juan Mac Donagh; Zsofia E. Kalman; Stefano Pascarelli; Nicolas Palopoli; László Dobson; Carmen Florencia Suarez; Kim Van Roey; Izabella Krystkowiak; Juan Esteban Griffin; Anurag Nagpal; Rajesh Bhardwaj; Francesca Diella; Bálint Mészáros; Kellie Dean; Norman E. Davey; Rita Pancsa; Lucía B. Chemes; Toby J. Gibson

doi:10.1093/nar/gkad1058

ELM-the Eukaryotic Linear Motif resource-2024 update

Manjeet Kumar
, Sushama Michael
, Jesús Alvarado-Valverde
, András Zeke
, Tamas Lazar
, Juliana Glavina
, Eszter Nagy-Kanta
, Juan Mac Donagh
, Zsofia E. Kalman
, Stefano Pascarelli
, Nicolas Palopoli
, László Dobson
, Carmen Florencia Suarez
, Kim Van Roey
, Izabella Krystkowiak
, Juan Esteban Griffin
, Anurag Nagpal
, Rajesh Bhardwaj
, Francesca Diella
, Bálint Mészáros

Kellie Dean, Norman E. Davey, Rita Pancsa, Lucía B. Chemes, Toby J. Gibson

School of Biochemistry and Cell Biology

European Molecular Biology Laboratory
Heidelberg University
Research Centre for Natural Sciences
Flanders Institute for Biotechnology
Vrije Universiteit Brussel
Universidad Nacional de San Martín (UNSAM)
Universidad Nacional de San Martin
Peter Pazmany Catholic University
Universidad Nacional de Quilmes
University of Lausanne
Swiss Federal Institute of Technology Zurich
Swiss Institute of Bioinformatics
Semmelweis University
Health Services Research
The Institute of Cancer Research
Birla Institute of Technology and Science Pilani
University of Bern
National Institutes of Health
St. Jude Children Research Hospital

Research output: Contribution to journal › Article › peer-review

Abstract

Short Linear Motifs (SLiMs)ãre the smallest str uct uralãnd functional components of modular eukaryotic proteins. Theyãreãlso the mostãbun- dant, especially when considering post-translational modifications. As wellãs being found throughout the cellãs part of regulatory processes, SLiMsãre e xtensiv ely mimick ed b y intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource isã representative (not comprehensiv e) database. T he ELM entriesãre created b yã gro wing community of skilledãnnotatorsãnd provideãn introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances inãreas ranging from innate immunity to both proteinãnd RNA degradation systems. In total, 39 classes of newlyãnnotated motifs have beenãdded,ãndãnother 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publicationsãnd including > 700 links to experimentally determined 3D str uct ures. Inã recent de v elopment, the InterPro protein module resource nowãlso includes ELM data. ELM isãvailableãt: http://elm.eu.org .

Original language	English
Pages (from-to)	D442-D455
Journal	Nucleic Acids Research
Volume	52
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkad1058
Publication status	Published - 5 Jan 2024

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1093/nar/gkad1058

Cite this

Kumar, M., Michael, S., Alvarado-Valverde, J., Zeke, A., Lazar, T., Glavina, J., Nagy-Kanta, E., Donagh, J. M., Kalman, Z. E., Pascarelli, S., Palopoli, N., Dobson, L., Suarez, C. F., Van Roey, K., Krystkowiak, I., Griffin, J. E., Nagpal, A., Bhardwaj, R., Diella, F., ... Gibson, T. J. (2024). ELM-the Eukaryotic Linear Motif resource-2024 update. Nucleic Acids Research, 52(D1), D442-D455. https://doi.org/10.1093/nar/gkad1058

@article{83f1dfcf1f8f4b97816b0d8635c91e43,

title = "ELM-the Eukaryotic Linear Motif resource-2024 update",

abstract = "Short Linear Motifs (SLiMs){\~a}re the smallest str uct ural{\~a}nd functional components of modular eukaryotic proteins. They{\~a}re{\~a}lso the most{\~a}bun- dant, especially when considering post-translational modifications. As well{\~a}s being found throughout the cell{\~a}s part of regulatory processes, SLiMs{\~a}re e xtensiv ely mimick ed b y intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource is{\~a} representative (not comprehensiv e) database. T he ELM entries{\~a}re created b y{\~a} gro wing community of skilled{\~a}nnotators{\~a}nd provide{\~a}n introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances in{\~a}reas ranging from innate immunity to both protein{\~a}nd RNA degradation systems. In total, 39 classes of newly{\~a}nnotated motifs have been{\~a}dded,{\~a}nd{\~a}nother 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publications{\~a}nd including > 700 links to experimentally determined 3D str uct ures. In{\~a} recent de v elopment, the InterPro protein module resource now{\~a}lso includes ELM data. ELM is{\~a}vailable{\~a}t: http://elm.eu.org .",

author = "Manjeet Kumar and Sushama Michael and Jes{\'u}s Alvarado-Valverde and Andr{\'a}s Zeke and Tamas Lazar and Juliana Glavina and Eszter Nagy-Kanta and Donagh, \{Juan Mac\} and Kalman, \{Zsofia E.\} and Stefano Pascarelli and Nicolas Palopoli and L{\'a}szl{\'o} Dobson and Suarez, \{Carmen Florencia\} and \{Van Roey\}, Kim and Izabella Krystkowiak and Griffin, \{Juan Esteban\} and Anurag Nagpal and Rajesh Bhardwaj and Francesca Diella and B{\'a}lint M{\'e}sz{\'a}ros and Kellie Dean and Davey, \{Norman E.\} and Rita Pancsa and Chemes, \{Luc{\'i}a B.\} and Gibson, \{Toby J.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023.",

year = "2024",

month = jan,

day = "5",

doi = "10.1093/nar/gkad1058",

language = "English",

volume = "52",

pages = "D442--D455",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Kumar, M, Michael, S, Alvarado-Valverde, J, Zeke, A, Lazar, T, Glavina, J, Nagy-Kanta, E, Donagh, JM, Kalman, ZE, Pascarelli, S, Palopoli, N, Dobson, L, Suarez, CF, Van Roey, K, Krystkowiak, I, Griffin, JE, Nagpal, A, Bhardwaj, R, Diella, F, Mészáros, B, Dean, K, Davey, NE, Pancsa, R, Chemes, LB & Gibson, TJ 2024, 'ELM-the Eukaryotic Linear Motif resource-2024 update', Nucleic Acids Research, vol. 52, no. D1, pp. D442-D455. https://doi.org/10.1093/nar/gkad1058

TY - JOUR

T1 - ELM-the Eukaryotic Linear Motif resource-2024 update

AU - Kumar, Manjeet

AU - Michael, Sushama

AU - Alvarado-Valverde, Jesús

AU - Zeke, András

AU - Lazar, Tamas

AU - Glavina, Juliana

AU - Nagy-Kanta, Eszter

AU - Donagh, Juan Mac

AU - Kalman, Zsofia E.

AU - Pascarelli, Stefano

AU - Palopoli, Nicolas

AU - Dobson, László

AU - Suarez, Carmen Florencia

AU - Van Roey, Kim

AU - Krystkowiak, Izabella

AU - Griffin, Juan Esteban

AU - Nagpal, Anurag

AU - Bhardwaj, Rajesh

AU - Diella, Francesca

AU - Mészáros, Bálint

AU - Dean, Kellie

AU - Davey, Norman E.

AU - Pancsa, Rita

AU - Chemes, Lucía B.

AU - Gibson, Toby J.

PY - 2024/1/5

Y1 - 2024/1/5

N2 - Short Linear Motifs (SLiMs)ãre the smallest str uct uralãnd functional components of modular eukaryotic proteins. Theyãreãlso the mostãbun- dant, especially when considering post-translational modifications. As wellãs being found throughout the cellãs part of regulatory processes, SLiMsãre e xtensiv ely mimick ed b y intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource isã representative (not comprehensiv e) database. T he ELM entriesãre created b yã gro wing community of skilledãnnotatorsãnd provideãn introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances inãreas ranging from innate immunity to both proteinãnd RNA degradation systems. In total, 39 classes of newlyãnnotated motifs have beenãdded,ãndãnother 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publicationsãnd including > 700 links to experimentally determined 3D str uct ures. Inã recent de v elopment, the InterPro protein module resource nowãlso includes ELM data. ELM isãvailableãt: http://elm.eu.org .

AB - Short Linear Motifs (SLiMs)ãre the smallest str uct uralãnd functional components of modular eukaryotic proteins. Theyãreãlso the mostãbun- dant, especially when considering post-translational modifications. As wellãs being found throughout the cellãs part of regulatory processes, SLiMsãre e xtensiv ely mimick ed b y intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource isã representative (not comprehensiv e) database. T he ELM entriesãre created b yã gro wing community of skilledãnnotatorsãnd provideãn introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances inãreas ranging from innate immunity to both proteinãnd RNA degradation systems. In total, 39 classes of newlyãnnotated motifs have beenãdded,ãndãnother 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publicationsãnd including > 700 links to experimentally determined 3D str uct ures. Inã recent de v elopment, the InterPro protein module resource nowãlso includes ELM data. ELM isãvailableãt: http://elm.eu.org .

UR - https://www.scopus.com/pages/publications/85181797305

U2 - 10.1093/nar/gkad1058

DO - 10.1093/nar/gkad1058

M3 - Article

C2 - 37962385

AN - SCOPUS:85181797305

SN - 0305-1048

VL - 52

SP - D442-D455

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

ELM-the Eukaryotic Linear Motif resource-2024 update

Abstract

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