Now showing items 1-14 of 14

    • A screen for novel targets casts polyphosphorylation of lysine as a common post-translational modification 

      Bentley-DeSousa, A; Moteshareie, H; Holinier, C; Tseng, Y-C; Bondy-Chorney, E; Davey, N; Golshani, A; Downey, M (2018-04)
    • An intrinsically disordered proteins community for ELIXIR 

      Davey, N; Babu, M; Blackledge, M; Bridge, A; Capella-Gutierrez, S; Dosztanyi, Z; Drysdale, R; Edwards, R; Elofsson, A; Felli, I; Gibson, T; Gutmanas, A; Hancock, J; Harrow, J; Higgins, D; Jeffries, C; Le Mercier, P; Mészáros, B; Necci, M; Notredame, C; Orchard, S; Ouzounis, C; Pancsa, R; Papaleo, E; Pierattelli, R; Piovesan, D; Promponas, V; Ruch, P; Rustici, G; Romero, P; Sarntivijai, S; Saunders, G; Schuler, B; Sharan, M; Shields, D; Sussman, J; Tedds, J; Tompa, P; Turewicz, M; Vondrasek, J; Vranken, W; Wallace, BA; Wichapong, K; Tosatto, S (2019-10-15)
      Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments ...
    • The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. 

      Palopoli, N; Iserte, JA; Chemes, LB; Marino-Buslje, C; Parisi, G; Gibson, TJ; Davey, NE (2020-01)
      Modern biology produces data at a staggering rate. Yet, much of these biological data is still isolated in the text, figures, tables and supplementary materials of articles. As a result, biological information created at ...
    • Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo. 

      Bandyopadhyay, S; Bhaduri, S; Örd, M; Davey, NE; Loog, M; Pryciak, PM (2020-11)
      Many protein-modifying enzymes recognize their substrates via docking motifs, but the range of functionally permissible motif sequences is often poorly defined. During eukaryotic cell division, cyclin-specific docking ...
    • DisProt: intrinsic protein disorder annotation in 2020 

      Hatos, A; Hajdu-Soltész, B; Monzon, AM; Palopoli, N; Álvarez, L; Aykac-Fas, B; Bassot, C; Benítez, GI; Bevilacqua, M; Chasapi, A; Chemes, L; Davey, NE; Davidović, R; Dunker, AK; Elofsson, A; Gobeill, J; Foutel, NSG; Sudha, G; Guharoy, M; Horvath, T; Iglesias, V; Kajava, AV; Kovacs, OP; Lamb, J; Lambrughi, M; Lazar, T; Leclercq, JY; Leonardi, E; Macedo-Ribeiro, S; Macossay-Castillo, M; Maiani, E; Manso, JA; Marino-Buslje, C; Martínez-Pérez, E; Mészáros, B; Mičetić, I; Minervini, G; Murvai, N; Necci, M; Ouzounis, CA; Pajkos, M; Paladin, L; Pancsa, R; Papaleo, E; Parisi, G; Pasche, E; Barbosa Pereira, PJ; Promponas, VJ; Pujols, J; Quaglia, F; Ruch, P; Salvatore, M; Schad, E; Szabo, B; Szaniszló, T; Tamana, S; Tantos, A; Veljkovic, N; Ventura, S; Vranken, W; Dosztányi, Z; Tompa, P; Tosatto, SCE; Piovesan, D
      <jats:title>Abstract</jats:title> <jats:p>The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report ...
    • ELM-the eukaryotic linear motif resource in 2020. 

      Kumar, M; Kumar, M; Gouw, M; Michael, S; Sámano-Sánchez, H; Pancsa, R; Glavina, J; Diakogianni, A; Valverde, JA; Bukirova, D; Čalyševa, J; Palopoli, N; Davey, NE; Chemes, LB; Gibson, TJ (2020-01)
      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 ...
    • ELM: the status of the 2010 eukaryotic linear motif resource. 

      Gould, CM; Diella, F; Via, A; Puntervoll, P; Gemünd, C; Chabanis-Davidson, S; Michael, S; Sayadi, A; Bryne, JC; Chica, C; Seiler, M; Davey, NE; Haslam, N; Weatheritt, RJ; Budd, A; Hughes, T; Pas, J; Rychlewski, L; Travé, G; Aasland, R; Helmer-Citterich, M; Linding, R; Gibson, TJ (2010-01)
      Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. ...
    • MobiDB: intrinsically disordered proteins in 2021. 

      Piovesan, D; Necci, M; Escobedo, N; Monzon, AM; Hatos, A; Mičetić, I; Quaglia, F; Paladin, L; Ramasamy, P; Dosztányi, Z; Vranken, WF; Davey, NE; Parisi, G; Fuxreiter, M; Tosatto, SCE
      The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, ...
    • Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1) 

      Balasuriya, N; Davey, NE; Johnson, JL; Liu, H; Biggar, KK; Cantley, LC; Li, SS-C; O'Donoghue, P (Elsevier BV, 2020-06)
    • PP1 and PP2A Use Opposite Phospho-dependencies to Control Distinct Processes at the Kinetochore. 

      Smith, RJ; Cordeiro, MH; Davey, NE; Vallardi, G; Ciliberto, A; Gross, F; Saurin, AT (2019-08)
      PP1 and PP2A-B56 are major serine/threonine phosphatase families that achieve specificity by colocalizing with substrates. At the kinetochore, however, both phosphatases localize to an almost identical molecular space and ...
    • SIRT3 controls brown fat thermogenesis by deacetylation regulation of pathways upstream of UCP1. 

      Sebaa, R; Johnson, J; Pileggi, C; Norgren, M; Xuan, J; Sai, Y; Tong, Q; Krystkowiak, I; Bondy-Chorney, E; Davey, NE; Krogan, N; Downey, M; Harper, M-E (2019-07)
      Objective Brown adipose tissue (BAT) is important for thermoregulation in many mammals. Uncoupling protein 1 (UCP1) is the critical regulator of thermogenesis in BAT. Here we aimed to investigate the deacetylation control ...
    • Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. 

      Wigington, CP; Roy, J; Damle, NP; Yadav, VK; Blikstad, C; Resch, E; Wong, CJ; Mackay, DR; Wang, JT; Krystkowiak, I; Bradburn, DA; Tsekitsidou, E; Hong, SH; Kaderali, MA; Xu, S-L; Stearns, T; Gingras, A-C; Ullman, KS; Ivarsson, Y; Davey, NE; Cyert, MS (2020-07-08)
      Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches ...
    • The functional importance of structure in unstructured protein regions. 

      Davey, NE (2019-06)
      After two decades of research, intrinsically disordered regions (IDRs) are established as a widespread phenomenon. The growing understanding of the significant functional role of IDRs has challenged the structure-function ...
    • The Mitotic Checkpoint Complex Requires an Evolutionary Conserved Cassette to Bind and Inhibit Active APC/C. 

      Di Fiore, B; Wurzenberger, C; Davey, NE; Pines, J (2016-12-08)
      The Spindle Assembly Checkpoint (SAC) ensures genomic stability by preventing sister chromatid separation until all chromosomes are attached to the spindle. It catalyzes the production of the Mitotic Checkpoint Complex ...