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The eukaryotic linear motif resource – 2018 update

Marc Gouw, Sushama Michael, Hugo Sámano-Sánchez, Manjeet Kumar, András Zeke, Benjamin Lang, Benoit Bely, Lucía B Chemes, Norman E Davey, Ziqi Deng, Francesca Diella, Clara-Marie Gürth (+9 others)
2017 Nucleic Acids Research  
The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover  ...  For 15 years, ELM has been one of the major resources for motif research.  ...  ACKNOWLEDGEMENTS We would like to thank all of the users of ELM for their continued interest and support, as well as the community of annotators for their time and efforts in keeping the database up to  ... 
doi:10.1093/nar/gkx1077 pmid:29136216 pmcid:PMC5753338 fatcat:zek2virp5nf2nf4mmrbtm352mu

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).  ...  In this update, we have added 21 novel motif classes, made major revisions to 12 motif classes and added >400 new instances mostly focused on DNA damage, the cytoskeleton, SH2-binding phosphotyrosine motifs  ...  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

iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains

Yaping Guo, Di Peng, Jiaqi Zhou, Shaofeng Lin, Chenwei Wang, Wanshan Ning, Haodong Xu, Wankun Deng, Yu Xue
2018 Nucleic Acids Research  
Here, we described the updated database iEKPD 2.0 (http://iekpd.biocuckoo.org) for eukaryotic protein kinases (PKs), protein phosphatases (PPs) and proteins containing phosphoprotein-binding domains (PPBDs  ...  We anticipate that iEKPD 2.0 represents a more useful resource for further study of phosphorylation regulators.  ...  ACKNOWLEDGEMENTS American Journal Experts reviewed the manuscript prior to submission. FUNDING  ... 
doi:10.1093/nar/gky1063 pmid:30380109 pmcid:PMC6324023 fatcat:ppn7xyocbfbbxbqf6nl4all3tq

Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs

Yangchun Frank Chen, Yu Xia
2021 Frontiers in Molecular Biosciences  
Moreover, in the absence of host-like domains or among pathogen proteins without domain assignment, effectors harbor a higher variety and density of short linear motifs targeting host domains that mediate  ...  DDIs exclusively in eukaryotes.  ...  Meanwhile, the Eukaryotic Linear Motif Resource currently contains ∼100 instances of bacteria-mimicked eukaryotic short linear motifs from a small number of extensively studied pathogenic species (Samano-Sanchez  ... 
doi:10.3389/fmolb.2021.626600 pmid:34012977 pmcid:PMC8126662 fatcat:g2q5ik73pbh2to4chagd4wnbsy

What We Learned From Big Data for Autophagy Research

Anne-Claire Jacomin, Lejla Gul, Padhmanand Sudhakar, Tamas Korcsmaros, Ioannis P. Nezis
2018 Frontiers in Cell and Developmental Biology  
The molecular mechanism of the autophagic machinery is well-described and has been extensively investigated.  ...  Autophagy is the process by which cytoplasmic components are engulfed in doublemembraned vesicles before being delivered to the lysosome to be degraded.  ...  LG is supported by the BBSRC Norwich Research Park Biosciences Doctoral Training Partnership (grant BB/M011216/1).  ... 
doi:10.3389/fcell.2018.00092 pmid:30175097 pmcid:PMC6107789 fatcat:3r2uparqf5ddflw324ys2e7xvy

The Spike Protein S1 Subunit of SARS-CoV-2 Contains an LxxIxE-like Motif that is Known to Recruit the Host PP2A-B56 Phosphatase [article]

Halim Maaroufi
2020 bioRxiv   pre-print
Here the analysis of CoV-2 S protein revealed in S1 subunit a B56-binding LxxIxE-like motif that could recruit the host protein phosphatase 2A (PP2A). This motif is absent in SARS-CoV and MERS-CoV.  ...  PP2A is a major family of serine/threonine phosphatases in eukaryotic cells. Phosphatases and kinases are big players in the regulation of pro-inflammatory responses during pathogenic infections.  ...  The eukaryotic linear motif resource -2018 update. Nucleic Acids Res., 46(D1), D428-259 D434. doi:10.1093/nar/gkx1077 260 Graham, R. L., & Baric, R. S. (2010).  ... 
doi:10.1101/2020.04.01.020941 fatcat:ghjf7ufvrvccrh6vvepvz3mcjy

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: The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 2007; 35(Web server issue): w455-9.  ...  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

ULK1 and ULK2 are less redundant than previously thought: Computational analysis uncovers distinct regulation and functions of these autophagy induction proteins [article]

Amanda Demeter, Mari Carmen Romero-Mulero, Luca Csabai, Márton Ölbei, Padhmanand Sudhakar, Wilfried Haerty, Tamás Korcsmáros
2020 bioRxiv   pre-print
We identified 18 ULK1-specific and 7 ULK2-specific protein motifs serving as different interaction interfaces.  ...  To understand the differences between ULK1 and ULK2, we compared the human ULK1 and ULK2 proteins and their regulation.  ...  The EMBL-EBI search and sequence analysis tools APIs in 2019. 491 Nucleic Acids Res. 47, W636-W641 (2019). 492 34. Gouw, M. et al. The eukaryotic linear motif resource -2018 update.  ... 
doi:10.1101/2020.02.27.967901 fatcat:gd4onv2q7jb6lkidorry23jju4

Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs [article]

Bishoy Wadie, Vitalii Kleshchevnikov, Elissavet Sandaltzopoulou, Caroline Benz, Evangelia Petsalaki
2021 bioRxiv   pre-print
of the human domain-linear motif code and the mechanisms of viral interference with this.  ...  Linear motifs have an integral role in dynamic cell functions including cell signalling, the cell cycle and others.  ...  Acknowledgments The authors would like to thank EMBL-EBI for funding this project and Ylva Ivarsson for input on the manuscript and validation.  ... 
doi:10.1101/2021.06.25.449930 fatcat:ibzy3veu2rfhhiqkmhgbafsioq

dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications

Kai-Yao Huang, Tzong-Yi Lee, Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang
2018 Nucleic Acids Research  
were subjected to motif discovery and functional enrichment analysis.  ...  This update highlights the current challenges in PTM crosstalk investigation and breaks the bottleneck of how proteomics may contribute to understanding PTM codes, revealing the next level of data complexity  ...  ACKNOWLEDGEMENTS The authors sincerely appreciate the Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen) for financially supporting this research.  ... 
doi:10.1093/nar/gky1074 pmid:30418626 fatcat:ggju4n675jci7hg52t7dxboeg4

PARSEC: PAtteRn SEarch and Contextualization

Alexis Allot, Yannick-Noël Anno, Laetitia Poidevin, Raymond Ripp, Olivier Poch, Odile Lecompte
2013 Computer applications in the biosciences : CABIOS  
We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic  ...  These modules allow the user to explore, visualize, filter and extract biological knowledge from a set of short genomic regions such as transcription factor binding sites.  ...  ACKNOWLEDGEMENTS The authors are grateful to Vincent Laudet and Ce´cile Rochette-Egly for helpful discussions during the development of PARSEC.  ... 
doi:10.1093/bioinformatics/btt455 pmid:23929031 fatcat:4a5dz23e3zcaph75slvnovi6ku

DeePromoter: Robust Promoter Predictor Using Deep Learning

Mhaned Oubounyt, Zakaria Louadi, Hilal Tayara, Kil To Chong
2019 Frontiers in Genetics  
In this work, we propose a robust deep learning model, called DeePromoter, to analyze the characteristics of the short eukaryotic promoter sequences, and accurately recognize the human and mouse promoter  ...  The promoter region is located near the transcription start sites and regulates transcription initiation of the gene by controlling the binding of RNA polymerase.  ...  Epd and epdnew, high-quality promoter resources in the next-generation sequencing era.  ... 
doi:10.3389/fgene.2019.00286 pmid:31024615 pmcid:PMC6460014 fatcat:sfcmmerpxre2rcpkeyr55pzhju

Learning the Regulatory Code of Gene Expression

Jan Zrimec, Filip Buric, Mariia Kokina, Victor Garcia, Aleksej Zelezniak
2021 Frontiers in Molecular Biosciences  
Here, we review the latest developments that apply shallow or deep learning to quantify molecular phenotypes and decode the cis-regulatory grammar from prokaryotic and eukaryotic sequencing data.  ...  of the gene and mRNA regulatory structures, achieving unprecedented performance.  ...  The authors from Rohs lab also provide an updated database of TFBS shape logos in 2020 (Chiu et al., 2020) .  ... 
doi:10.3389/fmolb.2021.673363 pmid:34179082 pmcid:PMC8223075 fatcat:xtrouhqxvnerlcrto63e734dwa

Minimotif Miner 4: a million peptide minimotifs and counting

Kenneth F Lyon, Xingyu Cai, Richard J Young, Abdullah-Al Mamun, Sanguthevar Rajasekaran, Martin R Schiller
2017 Nucleic Acids Research  
Minimotif Miner (MnM) is a database and web system for analyzing short functional peptide motifs, termed minimotifs.  ...  Another update is mapping human proteins and their minimotifs to know human variants from the dbSNP, build 150.  ...  ACKNOWLEDGEMENTS We thank the Nevada Institute of Personalized Medicine for use of their computers. FUNDING  ... 
doi:10.1093/nar/gkx1085 pmid:29140456 pmcid:PMC5753208 fatcat:4fslzqtq7zfe5bvzoclq4wqude

Conserved dual-mode gene regulation programs in higher eukaryotes

Jun-Yeong Lee, Jawon Song, Lucy LeBlanc, Ian Davis, Jonghwan Kim, Samuel Beck
2021 Nucleic Acids Research  
Here, through comparative epigenomic analyses, we demonstrate that the dual-mode gene regulation program is common in various eukaryotes, even in the species lacking CGIs.  ...  Altogether, our study establishes gene type divergence and the resulting dual-mode gene regulation as fundamental features shared in a broad range of higher eukaryotic species.  ...  Zynda for sharing the codes for methylation data analysis. We thank the Texas Advanced Computing Center (TACC) for providing HPC resources.  ... 
doi:10.1093/nar/gkab108 pmid:33621342 pmcid:PMC7969006 fatcat:ix7tszwv5bbhdmfvay6j5lwlfu
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