Search Results - "Gibson, Toby J"

A Million Peptide Motifs for the Molecular Biologist by Tompa, Peter, Davey, Norman E., Gibson, Toby J., Babu, M. Madan

“…A molecular description of functional modules in the cell is the focus of many high-throughput studies in the postgenomic era. A large portion of biomolecular…”
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The Eukaryotic Linear Motif resource: 2022 release by Kumar, Manjeet, Michael, Sushama, Alvarado-Valverde, Jesús, Mészáros, Bálint, Sámano‐Sánchez, Hugo, Zeke, András, Dobson, Laszlo, Lazar, Tamas, Örd, Mihkel, Nagpal, Anurag, Farahi, Nazanin, Käser, Melanie, Kraleti, Ramya, Davey, Norman E, Pancsa, Rita, Chemes, Lucía B, Gibson, Toby J

“…Abstract Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of…”
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Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction by Croset, Vincent, Rytz, Raphael, Cummins, Scott F, Budd, Aidan, Brawand, David, Kaessmann, Henrik, Gibson, Toby J, Benton, Richard

“…Ionotropic glutamate receptors (iGluRs) are a highly conserved family of ligand-gated ion channels present in animals, plants, and bacteria, which are best…”
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ELM—the eukaryotic linear motif resource in 2020 by Kumar, Manjeet, Gouw, Marc, Michael, Sushama, Sámano-Sánchez, Hugo, Pancsa, Rita, Glavina, Juliana, Diakogianni, Athina, Valverde, Jesús Alvarado, Bukirova, Dayana, Čalyševa, Jelena, Palopoli, Nicolas, Davey, Norman E, Chemes, Lucía B, Gibson, Toby J

“…Abstract The eukaryotic linear motif (ELM) resource is a repository of manually curated experimentally validated short linear motifs (SLiMs). Since the initial…”
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The ABBA Motif Binds APC/C Activators and Is Shared by APC/C Substrates and Regulators by Di Fiore, Barbara, Davey, Norman E., Hagting, Anja, Izawa, Daisuke, Mansfeld, Jörg, Gibson, Toby J., Pines, Jonathon

“…The anaphase-promoting complex or cyclosome (APC/C) is the ubiquitin ligase that regulates mitosis by targeting specific proteins for degradation at specific…”
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Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation by Van Roey, Kim, Uyar, Bora, Weatheritt, Robert J, Dinkel, Holger, Seiler, Markus, Budd, Aidan, Gibson, Toby J, Davey, Norman E

“…The authors examine short linear motifs with regard to ubiquitous and functionally diverse protein interaction modules directing cell regulation…”
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega by Sievers, Fabian, Wilm, Andreas, Dineen, David, Gibson, Toby J, Karplus, Kevin, Li, Weizhong, Lopez, Rodrigo, McWilliam, Hamish, Remmert, Michael, Söding, Johannes, Thompson, Julie D, Higgins, Desmond G

“…Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These…”
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Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents by Zeke, Andras, Gibson, Toby J, Dobson, Laszlo

“…The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately,…”
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A Proteome-wide Screen for Mammalian SxIP Motif-Containing Microtubule Plus-End Tracking Proteins by Jiang, Kai, Toedt, Grischa, Montenegro Gouveia, Susana, Davey, Norman E., Hua, Shasha, van der Vaart, Babet, Grigoriev, Ilya, Larsen, Jesper, Pedersen, Lotte B., Bezstarosti, Karel, Lince-Faria, Mariana, Demmers, Jeroen, Steinmetz, Michel O., Gibson, Toby J., Akhmanova, Anna

“…Microtubule plus-end tracking proteins (+TIPs) are structurally and functionally diverse factors that accumulate at the growing microtubule plus-ends, connect…”
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Motif switches: decision-making in cell regulation by Van Roey, Kim, Gibson, Toby J, Davey, Norman E

“…► The functionality of IDRs is in part determined by short linear motifs. ► The intrinsic properties of SLiMs enable them to mediate molecular switching. ►…”
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The eukaryotic linear motif resource - 2018 update by Gouw, Marc, Michael, Sushama, Sámano-Sánchez, Hugo, Kumar, Manjeet, Zeke, András, Lang, Benjamin, Bely, Benoit, Chemes, Lucía B, Davey, Norman E, Deng, Ziqi, Diella, Francesca, Gürth, Clara-Marie, Huber, Ann-Kathrin, Kleinsorg, Stefan, Schlegel, Lara S, Palopoli, Nicolás, Roey, Kim V, Altenberg, Brigitte, Reményi, Attila, Dinkel, Holger, Gibson, Toby J

“…Abstract Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly…”
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The eukaryotic linear motif resource ELM: 10 years and counting by Dinkel, Holger, Van Roey, Kim, Michael, Sushama, Davey, Norman E, Weatheritt, Robert J, Born, Diana, Speck, Tobias, Krüger, Daniel, Grebnev, Gleb, Kuban, Marta, Strumillo, Marta, Uyar, Bora, Budd, Aidan, Altenberg, Brigitte, Seiler, Markus, Chemes, Lucía B, Glavina, Juliana, Sánchez, Ignacio E, Diella, Francesca, Gibson, Toby J

“…The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs)…”
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ELM—the Eukaryotic Linear Motif resource—2024 update by Kumar, Manjeet, Michael, Sushama, Alvarado-Valverde, Jesús, Zeke, András, Lazar, Tamas, Glavina, Juliana, Nagy-Kanta, Eszter, Donagh, Juan Mac, Kalman, Zsofia E, Pascarelli, Stefano, Palopoli, Nicolas, Dobson, László, Suarez, Carmen Florencia, Van Roey, Kim, Krystkowiak, Izabella, Griffin, Juan Esteban, Nagpal, Anurag, Bhardwaj, Rajesh, Diella, Francesca, Mészáros, Bálint, Dean, Kellie, Davey, Norman E, Pancsa, Rita, Chemes, Lucía B, Gibson, Toby J

“…Abstract Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They are also the most abundant,…”
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Unveiling the Complexity of cis-Regulation Mechanisms in Kinases: A Comprehensive Analysis by Navarro, Alvaro M, Alonso, Macarena, Martínez-Pérez, Elizabeth, Lazar, Tamas, Gibson, Toby J, Iserte, Javier A, Tompa, Peter, Marino-Buslje, Cristina

“…Protein cis-regulatory elements (CREs) are regions that modulate the activity of a protein through intramolecular interactions. Kinases, pivotal enzymes in…”
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Drift and conservation of differential exon usage across tissues in primate species by Reyes, Alejandro, Anders, Simon, Weatheritt, Robert J., Gibson, Toby J., Steinmetz, Lars M., Huber, Wolfgang

“…Alternative usage of exons provides genomes with plasticity to produce different transcripts from the same gene, modulating the function, localization, and…”
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Linear motifs confer functional diversity onto splice variants by Weatheritt, Robert J, Davey, Norman E, Gibson, Toby J

“…The pre-translational modification of messenger ribonucleic acids (mRNAs) by alternative promoter usage and alternative splicing is an important source of…”
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Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation by Lee, Chop Yan, Hubrich, Dalmira, Varga, Julia K, Schäfer, Christian, Welzel, Mareen, Schumbera, Eric, Djokic, Milena, Strom, Joelle M, Schönfeld, Jonas, Geist, Johanna L, Polat, Feyza, Gibson, Toby J, Keller Valsecchi, Claudia Isabelle, Kumar, Manjeet, Schueler-Furman, Ora, Luck, Katja

“…Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural…”
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Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors by Pabis, Marta, Corsini, Lorenzo, Vincendeau, Michelle, Tripsianes, Konstantinos, Gibson, Toby J, Brack-Werner, Ruth, Sattler, Michael

“…Abstract The HIV-1 protein Rev is essential for virus replication and ensures the expression of partially spliced and unspliced transcripts. We identified a…”
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The switches.ELM resource: a compendium of conditional regulatory interaction interfaces by Van Roey, Kim, Dinkel, Holger, Weatheritt, Robert J, Gibson, Toby J, Davey, Norman E

“…Short linear motifs (SLiMs) are protein interaction sites that play an important role in cell regulation by controlling protein activity, localization, and…”
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Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity by Palopoli, Nicolás, González Foutel, Nicolás S, Gibson, Toby J, Chemes, Lucía B

“…Abstract Pocket proteins retinoblastoma (pRb), p107 and p130 are negative regulators of cellular proliferation and multifunctional proteins regulating…”
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