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The eukaryotic linear motif resource ELM: 10 years and counting

Holger Dinkel, Kim Van Roey, Sushama Michael, Norman E. Davey, Robert J. Weatheritt, Diana Born, Tobias Speck, Daniel Krüger, Gleb Grebnev, Marta Kubań, Marta Strumillo, Bora Uyar (+8 others)
2013 Nucleic Acids Research  
The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs).  ...  For >10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs.  ...  ACKNOWLEDGEMENTS The authors would like to thank the users of the ELM resource for their longstanding support as well as colleagues and annotators for their contributions and feedback to the ELM database  ... 
doi:10.1093/nar/gkt1047 pmid:24214962 pmcid:PMC3964949 fatcat:boz7kpa2xfb2dkjhffkva4racm

ELM-the eukaryotic linear motif resource in 2020

2019 Nucleic Acids Research  
The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs).  ...  Since the initial release almost 20 years ago, ELM has become an indispensable resource for the molecular biology community for investigating functional regions in many proteins.  ...  ACKNOWLEDGEMENTS We thank the ELM resource users for their interest and the value it places on our work.  ... 
doi:10.1093/nar/gkz1030 pmid:31680160 pmcid:PMC7145657 fatcat:m7mta2yzcbhpbhi6mxdrcxd7me

ELM--the database of eukaryotic linear motifs

H. Dinkel, S. Michael, R. J. Weatheritt, N. E. Davey, K. Van Roey, B. Altenberg, G. Toedt, B. Uyar, M. Seiler, A. Budd, L. Jodicke, M. A. Dammert (+17 others)
2011 Nucleic Acids Research  
The Eukaryotic Linear Motif (ELM) resource at http:// elm.eu.org provides the biological community with a comprehensive database of known experimentally validated motifs, and an exploratory tool to discover  ...  Schema of the ELM resource and data life cycle. Annotated ELM classes, and instances thereof, can be searched by database query.  ...  ACKNOWLEDGEMENTS The authors would like to thank the users of the ELM resource as well as all colleagues, contributors and annotators of the ELM resource.  ... 
doi:10.1093/nar/gkr1064 pmid:22110040 pmcid:PMC3245074 fatcat:x5kvgzrrnrhczcdxvtm6zoetiq

Prediction of virus-host protein-protein interactions mediated by short linear motifs

Andrés Becerra, Victor A. Bucheli, Pedro A. Moreno
2017 BMC Bioinformatics  
We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions.  ...  With respect to HIV-1, the sets C ∪R, D∪R, C ∪D∪R infer all known interactions between HIV1 and human proteins med iated by linear motifs.  ...  Irene Tischer and Angel García for their valuable input and comments at initial stages of the research.  ... 
doi:10.1186/s12859-017-1570-7 pmid:28279163 pmcid:PMC5345135 fatcat:5mtkw6o2krgpfl42yc2pk3nbem

Linear motifs confer functional diversity onto splice variants

Robert J. Weatheritt, Norman E. Davey, Toby J. Gibson
2012 Nucleic Acids Research  
We find that regions removed or included by pre-translational variation are enriched in linear motifs suggesting that the removal or inclusion of exons containing these interaction modules is an important  ...  In particular, we observe that PDZ-, PTB-, SH2-and WW-domain binding motifs are more likely to occur within alternative exons.  ...  ACKNOWLEDGEMENTS The authors thank members of the Gibson Team, and in particular Kim Van Roey, for their critical reading of the manuscript.  ... 
doi:10.1093/nar/gks442 pmid:22638587 pmcid:PMC3424572 fatcat:7u4o6iovkfgwxg3ptt2makynya

Whole Exome Sequencing Reveals a Novel AUTS2 In-Frame Deletion in a Boy with Global Developmental Delay, Absent Speech, Dysmorphic Features, and Cerebral Anomalies

Pietro Palumbo, Ester Di Muro, Maria Accadia, Mario Benvenuto, Marilena Carmela Di Giacomo, Stefano Castellana, Tommaso Mazza, Marco Castori, Orazio Palumbo, Massimo Carella
2021 Genes  
We describes a 9-year-old boy with global developmental delay, absent speech, minor craniofacial anomalies, hypoplasia of the cerebellar vermis and thinning of the corpus callosum, resulted carrier of  ...  Notably, our patient is the first reported so far in medical literature carrying an in-frame deletion and the first in which absent language, hypoplasia of the cerebellar vermis and thinning of the corpus  ...  Then, the reference FASTA sequence (Uniprot accession: Q8WXX7-1) was scanned for the presence of Eukaryotic Linear Motifs (ELM), using the ELM web-service (http://elm.eu.org/ (accessed on 1 February 2021  ... 
doi:10.3390/genes12020229 pmid:33562463 fatcat:omejvzzshvhfxfvm37pl36k23a

Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease

André M. Comeau, Josée Dufour, Guillaume F. Bouvet, Volker Jacobi, Martha Nigg, Bernard Henrissat, Jérôme Laroche, Roger C. Levesque, Louis Bernier
2014 Genome Biology and Evolution  
The ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years.  ...  Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted.  ...  Acknowledgments The authors thank Mialy Rabemanantsoa, our colleagues at the IBIS/Université Laval Plate-forme d'Analyses Gé nomiques and the McGill University/Gé nome Qué bec Innovation Centre for technical  ... 
doi:10.1093/gbe/evu281 pmid:25539722 pmcid:PMC4350166 fatcat:uhchzzfaozdazj5fay5fotcvoa

Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins

Heidy Elkhaligy, Christian A. Balbin, Jessica L. Gonzalez, Teresa Liberatore, Jessica Siltberg-Liberles
2021 Viruses  
One mechanism of interaction is viral mimicry through short linear motifs (SLiMs) that act as functional signatures in host proteins.  ...  The overlap between rapidly evolving protein regions and the location of functionally critical SLiMs suggest that these motifs and their functional potential may be rapidly rewired causing variation in  ...  Acknowledgments: Thanks to Janelle Nunez-Castilla for helpful edits and comments on the review article and to Daniel Morales for assistance in the lab.  ... 
doi:10.3390/v13122369 pmid:34960638 pmcid:PMC8703344 fatcat:isygycgcgnesnngpz4geiz5qzy

Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins

Marco Necci, Damiano Piovesan, Silvio C E Tosatto
2018 Database: The Journal of Biological Databases and Curation  
The recent update of MobiDB presented the opportunity to carry out an in-depth comparison of the content of these validated ID collections, namely DIBS, DisProt, IDEAL, MFIB, FuzDB, ELM and UniProt.  ...  Despite that, the majority of the considered features are not statistically different across databases, with the exception of ELM. FuzDB also shares half of its entries with DisProt.  ...  Funding This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement [778247]. Conflicts of interest.  ... 
doi:10.1093/database/bay127 pmid:30576490 pmcid:PMC6301333 fatcat:be6fknrywfckvdwkjxbq6uzxci

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks

Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards
2015 F1000Research  
Dinkel H, Van Roey K, Michael S, et al.: The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res. 2014; 42(Database issue): D259-66.  ...  Davey NE, Edwards RJ, Shields DC: Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins.  ...  Acknowledgments The authors would like to thank the UNSW Science Faculty Computing Unit for all their assistance in setting up the SLiMSuite REST servers.  ... 
doi:10.12688/f1000research.6773.1 pmid:26674271 pmcid:PMC4670012 fatcat:rhwosiio4vdnbdach6pycih65i

NSort/DB: An Intranuclear Compartment Protein Database

Kai Willadsen, Nurul Mohamad, Mikael Bodén
2012 Genomics, Proteomics & Bioinformatics  
The database is searchable by protein identifier or compartment, and has a documented web service API.  ...  The search interface, web service and data download are all freely available online at http://www.nsort.org/db/.  ...  Acknowledgements The authors acknowledge funding and support from the Australian Research Council Centre of Excellence in Bioinformatics.  ... 
doi:10.1016/j.gpb.2012.07.001 pmid:23084778 pmcid:PMC5054713 fatcat:5gob52ohwbgbfotgsqol7f2izm

Minimotif miner 2nd release: a database and web system for motif search

S. Rajasekaran, S. Balla, P. Gradie, M. R. Gryk, K. Kadaveru, V. Kundeti, M. W. Maciejewski, T. Mi, N. Rubino, J. Vyas, M. R. Schiller
2009 Nucleic Acids Research  
We have revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions.  ...  Minimotif Miner (MnM) consists of a minimotif database and a web-based application that enables prediction of motif-based functions in user-supplied protein queries.  ...  The MnM database and webtool are complementary to other major systems for minimotif prediction. Eukaryotic Linear Motif Resource (ELM) and Scansite have a more limited set of minimotifs.  ... 
doi:10.1093/nar/gkn865 pmid:18978024 pmcid:PMC2686579 fatcat:4ka2yk7puzehxfrstogox5oiou

Computational Prediction of Short Linear Motifs from Protein Sequences [chapter]

Richard J. Edwards, Nicolas Palopoli
2014 Msphere  
Abbreviations DMI Domain-motif interaction ELM Eukaryotic linear motif FPR False positive rate GO Gene ontology HMM Hidden Markov model IDP Intrinsically disordered protein 90 IDR Intrinsically disordered  ...  Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another.  ...  The Eukaryotic Linear Motif (ELM) database is now over 10 years old [ 9 ] and the number of annotated ELMs (as of Jan 2014) has increased to nearly 200 classes and over 2,400 instances in six categories  ... 
doi:10.1007/978-1-4939-2285-7_6 pmid:25555723 fatcat:ix4mi5e325gmdctjousi4szhey

Computational identification and analysis of protein short linear motifs

Norman, E. Davey
2010 Frontiers in Bioscience  
The distribution of counts, for all 132 motif classes in the ELM database, against the number of residues inspected before 1 instance of a given ELM would be expected by chance.  ...  Figure 2 . 2 Comparison of the relative local conservation (RLC) scores (38) of ELM (motif) and Non-ELM (all other) residues for ELM-containing proteins in the ELM database.  ... 
doi:10.2741/3647 pmid:20515727 fatcat:kgnnws4ohveddbszl2slonklge

PhD Thesis: Characterizing Viruses Mimicry Mechanisms with Protein-Protein Interactions and Short Linear Motifs

Andrés Becerra Sandoval
2017 Figshare  
The result of this thesis is a computational method and platform for predicting interactions between host and viral proteins mediated by linear motifs. This candida [...]  ...  This thesis is about predicting virus-host interactions mediated by protein short linear motifs.  ...  The database for SLiMs in eukaryotes is ELM, standing for the eukaryotic linear motifs resource for functional sites in proteins [51] .  ... 
doi:10.6084/m9.figshare.5398630.v1 fatcat:5keirdnlhbc5zcsagvhpzxsppe
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