Norman Davey - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/gibson/members/index.php?s_personId=5193

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 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, ... ... Davey NE, et al. ELM-the Eukaryotic Linear Motif resource-2024 update. Nucleic Acids Research. PMID 37962385 DOI: 10.1093/nar/gkad1058  0.693
2023 Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nature Communications. 14: 5636. PMID 37704626 DOI: 10.1038/s41467-023-41312-8  0.364
2023 Kotb HM, Davey NE. xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures. Biomolecules. 13. PMID 37371487 DOI: 10.3390/biom13060906  0.399
2023 Kliche J, Garvanska DH, Simonetti L, Badgujar D, Dobritzsch D, Nilsson J, Davey NE, Ivarsson Y. Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions. Molecular Systems Biology. e11164. PMID 37219487 DOI: 10.15252/msb.202211164  0.435
2023 Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Current Opinion in Structural Biology. 80: 102593. PMID 37099901 DOI: 10.1016/j.sbi.2023.102593  0.402
2022 Madhu P, Davey NE, Ivarsson Y. How viral proteins bind short linear motifs and intrinsically disordered domains. Essays in Biochemistry. PMID 36504386 DOI: 10.1042/EBC20220047  0.401
2022 Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, ... ... Davey NE, et al. A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology. PMID 36344848 DOI: 10.1038/s41594-022-00849-w  0.321
2022 Benz C, Ali M, Krystkowiak I, Simonetti L, Sayadi A, Mihalic F, Kliche J, Andersson E, Jemth P, Davey NE, Ivarsson Y. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Molecular Systems Biology. 18: e10584. PMID 35044719 DOI: 10.15252/msb.202110584  0.403
2021 Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, ... ... Davey NE, et al. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Research. PMID 34850135 DOI: 10.1093/nar/gkab1082  0.348
2021 Kruse T, Benz C, Garvanska DH, Lindqvist R, Mihalic F, Coscia F, Inturi R, Sayadi A, Simonetti L, Nilsson E, Ali M, Kliche J, Moliner Morro A, Mund A, Andersson E, ... ... Davey NE, et al. Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities. Nature Communications. 12: 6761. PMID 34799561 DOI: 10.1038/s41467-021-26498-z  0.328
2021 Kumar M, Michael S, Alvarado-Valverde J, Mészáros B, Sámano-Sánchez H, Zeke A, Dobson L, Lazar T, Örd M, Nagpal A, Farahi N, Käser M, Kraleti R, Davey NE, Pancsa R, et al. The Eukaryotic Linear Motif resource: 2022 release. Nucleic Acids Research. PMID 34718738 DOI: 10.1093/nar/gkab975  0.642
2020 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. MobiDB: intrinsically disordered proteins in 2021. Nucleic Acids Research. PMID 33237329 DOI: 10.1093/nar/gkaa1058  0.377
2020 Bandyopadhyay S, Bhaduri S, Örd M, Davey NE, Loog M, Pryciak PM. Comprehensive Analysis of G1 Cyclin Docking Motif Sequences that Control CDK Regulatory Potency In Vivo. Current Biology : Cb. PMID 32976810 DOI: 10.1016/j.cub.2020.08.099  0.316
2020 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 SL, ... ... Davey NE, et al. Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. Molecular Cell. PMID 32645368 DOI: 10.1016/J.Molcel.2020.06.029  0.361
2020 Palopoli N, Iserte JA, Chemes LB, Marino-Buslje C, Parisi G, Gibson TJ, Davey NE. The articles.ELM resource: simplifying access to protein linear motif literature by annotation, text-mining and classification. Database : the Journal of Biological Databases and Curation. 2020. PMID 32507889 DOI: 10.1093/Database/Baaa040  0.585
2020 Piovesan D, Tosatto S, Dosztanyi Z, Davey N. The intrinsically disordered proteins community roadmap F1000research. 9. DOI: 10.7490/F1000Research.1117972.1  0.376
2019 Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, et al. An intrinsically disordered proteins community for ELIXIR. F1000research. 8. PMID 31824649 DOI: 10.12688/F1000Research.20136.1  0.718
2019 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, et al. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Research. PMID 31713636 DOI: 10.1093/Nar/Gkz975  0.329
2019 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. ELM-the eukaryotic linear motif resource in 2020. Nucleic Acids Research. PMID 31680160 DOI: 10.1093/Nar/Gkz1030  0.667
2019 Ueki Y, Kruse T, Weisser MB, Sundell GN, Larsen MSY, Mendez BL, Jenkins NP, Garvanska DH, Cressey L, Zhang G, Davey N, Montoya G, Ivarsson Y, Kettenbach AN, Nilsson J. A Consensus Binding Motif for the PP4 Protein Phosphatase. Molecular Cell. PMID 31585692 DOI: 10.1016/J.Molcel.2019.08.029  0.485
2019 Jespersen N, Estelle A, Waugh N, Davey NE, Blikstad C, Ammon YC, Akhmanova A, Ivarsson Y, Hendrix DA, Barbar E. Systematic identification of recognition motifs for the hub protein LC8. Life Science Alliance. 2. PMID 31266884 DOI: 10.26508/lsa.201900366  0.357
2019 Bridge A, Davey N, Dosztanyi Z, Finn R, Martin M, Orchard S, Tosatto S, Velankar S. Integration and standardisation of intrinsically disordered protein data F1000research. 8. DOI: 10.7490/F1000Research.1117015.1  0.411
2018 Krystkowiak I, Manguy J, Davey NE. PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants. Nucleic Acids Research. PMID 29873773 DOI: 10.1093/nar/gky426  0.471
2018 Bentley-DeSousa A, Holinier C, Moteshareie H, Tseng YC, Kajjo S, Nwosu C, Amodeo GF, Bondy-Chorney E, Sai Y, Rudner A, Golshani A, Davey NE, Downey M. A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis. Cell Reports. 22: 3427-3439. PMID 29590613 DOI: 10.1016/J.Celrep.2018.02.104  0.344
2018 Chhabra S, Fischer P, Takeuchi K, Dubey A, Ziarek JJ, Boeszoermenyi A, Mathieu D, Bermel W, Davey NE, Wagner G, Arthanari H. N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 29432148 DOI: 10.1073/Pnas.1717560115  0.303
2017 Piovesan D, Tabaro F, Paladin L, Necci M, Micetic I, Camilloni C, Davey N, Dosztányi Z, Mészáros B, Monzon AM, Parisi G, Schad E, Sormanni P, Tompa P, Vendruscolo M, et al. MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Research. PMID 29136219 DOI: 10.1093/Nar/Gkx1071  0.404
2017 Gouw M, Michael S, Sámano-Sánchez H, Kumar M, Zeke A, Lang B, Bely B, Chemes LB, Davey NE, Deng Z, Diella F, Gürth CM, Huber AK, Kleinsorg S, Schlegel LS, et al. The eukaryotic linear motif resource - 2018 update. Nucleic Acids Research. PMID 29136216 DOI: 10.1093/Nar/Gkx1077  0.696
2017 Krystkowiak I, Davey NE. SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. Nucleic Acids Research. PMID 28387819 DOI: 10.1093/nar/gkx238  0.513
2016 Davey NE, Seo MH, Yadav VK, Jeon J, Nim S, Krystkowiak I, Blikstad C, Dong D, Markova N, Kim PM, Ivarsson Y. Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome. The Febs Journal. PMID 28002650 DOI: 10.1111/febs.13995  0.418
2016 Manguy J, Jehl P, Dillon ET, Davey NE, Shields DC, Holton TA. Peptigram: A Web-Based Application for Peptidomics Data Visualization. Journal of Proteome Research. PMID 27997202 DOI: 10.1021/Acs.Jproteome.6B00751  0.725
2016 Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27965415 DOI: 10.1093/Nar/Gkw1279  0.339
2016 Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, et al. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. PMID 27899601 DOI: 10.1093/Nar/Gkw1056  0.366
2016 Hertz EP, Kruse T, Davey NE, López-Méndez B, Sigurðsson JO, Montoya G, Olsen JV, Nilsson J. A Conserved Motif Provides Binding Specificity to the PP2A-B56 Phosphatase. Molecular Cell. PMID 27453045 DOI: 10.1016/j.molcel.2016.06.024  0.369
2016 Jehl P, Manguy J, Shields DC, Higgins DG, Davey NE. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Research. PMID 27085803 DOI: 10.1093/Nar/Gkw265  0.635
2016 Davey N. Discovery and Characterisation of Novel Functional Modules in Intrinsically Disordered Regions Biophysical Journal. 110: 2a. DOI: 10.1016/J.Bpj.2015.11.053  0.447
2015 Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Communication and Signaling : Ccs. 13: 45. PMID 26626130 DOI: 10.1186/s12964-015-0123-9  0.307
2015 Dinkel H, Van Roey K, Michael S, Kumar M, Uyar B, Altenberg B, Milchevskaya V, Schneider M, Kühn H, Behrendt A, Dahl SL, Damerell V, Diebel S, Kalman S, Klein S, ... ... Davey NE, et al. ELM 2016-data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Research. PMID 26615199 DOI: 10.1093/Nar/Gkv1291  0.631
2015 Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Communication and Signaling : Ccs. 13: 43. PMID 26589632 DOI: 10.1186/S12964-015-0120-Z  0.459
2015 Di Fiore B, Davey NE, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J. The ABBA motif binds APC/C activators and is shared by APC/C substrates and regulators. Developmental Cell. 32: 358-72. PMID 25669885 DOI: 10.1016/J.Devcel.2015.01.003  0.526
2014 Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ. Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? Molecular Biosystems. 10: 2626-42. PMID 25057855 DOI: 10.1039/C4Mb00290C  0.513
2014 Tompa P, Davey NE, Gibson TJ, Babu MM. A million peptide motifs for the molecular biologist. Molecular Cell. 55: 161-9. PMID 25038412 DOI: 10.1016/J.Molcel.2014.05.032  0.572
2014 Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chemical Reviews. 114: 6733-78. PMID 24926813 DOI: 10.1021/Cr400585Q  0.787
2014 Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, et al. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Research. 42: D259-66. PMID 24214962 DOI: 10.1093/Nar/Gkt1047  0.777
2013 Pushker R, Mooney C, Davey NE, Jacqué JM, Shields DC. Marked variability in the extent of protein disorder within and between viral families. Plos One. 8: e60724. PMID 23620725 DOI: 10.1371/Journal.Pone.0060724  0.528
2013 Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ, Davey NE. The switches.ELM resource: a compendium of conditional regulatory interaction interfaces. Science Signaling. 6: rs7. PMID 23550212 DOI: 10.1126/Scisignal.2003345  0.619
2012 Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N. EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. Journal of Proteome Research. 11: 6056-65. PMID 23098558 DOI: 10.1021/Pr300721F  0.574
2012 Naumer M, Sonntag F, Schmidt K, Nieto K, Panke C, Davey NE, Popa-Wagner R, Kleinschmidt JA. Properties of the adeno-associated virus assembly-activating protein. Journal of Virology. 86: 13038-48. PMID 23015698 DOI: 10.1128/Jvi.01675-12  0.336
2012 Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Research. 40: 10628-41. PMID 22977176 DOI: 10.1093/Nar/Gks854  0.783
2012 Stavropoulos I, Khaldi N, Davey NE, O'Brien K, Martin F, Shields DC. Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins. Plos One. 7: e44389. PMID 22962613 DOI: 10.1371/Journal.Pone.0044389  0.602
2012 Jiang K, Toedt G, Montenegro Gouveia S, Davey NE, Hua S, van der Vaart B, Grigoriev I, Larsen J, Pedersen LB, Bezstarosti K, Lince-Faria M, Demmers J, Steinmetz MO, Gibson TJ, Akhmanova A. A Proteome-wide screen for mammalian SxIP motif-containing microtubule plus-end tracking proteins. Current Biology : Cb. 22: 1800-7. PMID 22885064 DOI: 10.1016/J.Cub.2012.07.047  0.648
2012 Weatheritt RJ, Davey NE, Gibson TJ. Linear motifs confer functional diversity onto splice variants. Nucleic Acids Research. 40: 7123-31. PMID 22638587 DOI: 10.1093/Nar/Gks442  0.654
2012 Van Roey K, Gibson TJ, Davey NE. Motif switches: decision-making in cell regulation. Current Opinion in Structural Biology. 22: 378-85. PMID 22480932 DOI: 10.1016/J.Sbi.2012.03.004  0.592
2012 Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ. The identification of short linear motif-mediated interfaces within the human interactome. Bioinformatics (Oxford, England). 28: 976-82. PMID 22328783 DOI: 10.1093/Bioinformatics/Bts072  0.669
2012 Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, et al. ELM--the database of eukaryotic linear motifs. Nucleic Acids Research. 40: D242-51. PMID 22110040 DOI: 10.1093/Nar/Gkr1064  0.812
2012 Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. Attributes of short linear motifs. Molecular Biosystems. 8: 268-81. PMID 21909575 DOI: 10.1039/C1Mb05231D  0.75
2012 Edwards RJ, Davey NE, O'Brien K, Shields DC. Interactome-wide prediction of short, disordered protein interaction motifs in humans. Molecular Biosystems. 8: 282-95. PMID 21879107 DOI: 10.7490/F1000Research.1089989.1  0.728
2011 Mooney C, Davey N, Martin AJ, Walsh I, Shields DC, Pollastri G. In silico protein motif discovery and structural analysis. Methods in Molecular Biology (Clifton, N.J.). 760: 341-53. PMID 21780007 DOI: 10.1007/978-1-61779-176-5_21  0.673
2011 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Research. 39: W56-60. PMID 21622654 DOI: 10.1093/Nar/Gkr402  0.835
2011 Davey NE, Travé G, Gibson TJ. How viruses hijack cell regulation. Trends in Biochemical Sciences. 36: 159-69. PMID 21146412 DOI: 10.1016/J.Tibs.2010.10.002  0.569
2010 Davey NE, Edwards RJ, Shields DC. Computational identification and analysis of protein short linear motifs. Frontiers in Bioscience (Landmark Edition). 15: 801-25. PMID 20515727 DOI: 10.2741/3647  0.74
2010 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Research. 38: W534-9. PMID 20497999 DOI: 10.1093/Nar/Gkq440  0.824
2010 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. Bmc Bioinformatics. 11: 14. PMID 20055997 DOI: 10.1186/1471-2105-11-14  0.708
2010 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, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research. 38: D167-80. PMID 19920119 DOI: 10.1093/Nar/Gkp1016  0.802
2010 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch: A webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6282: 50-61. DOI: 10.1007/978-3-642-16001-1_5  0.814
2009 Davey NE, Shields DC, Edwards RJ. Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics (Oxford, England). 25: 443-50. PMID 19136552 DOI: 10.1093/Bioinformatics/Btn664  0.736
2008 Casey FP, Davey NE, Baran I, Varekova RS, Shields DC. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). Journal of Chemical Information and Modeling. 48: 1524-9. PMID 18570372 DOI: 10.1021/Ci8000474  0.596
2008 Edwards RJ, Davey NE, Shields DC. CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics (Oxford, England). 24: 1307-9. PMID 18375965 DOI: 10.1093/Bioinformatics/Btn105  0.693
2007 Edwards RJ, Davey NE, Shields DC. SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. Plos One. 2: e967. PMID 17912346 DOI: 10.1371/Journal.Pone.0000967  0.704
2007 Davey NE, Edwards RJ, Shields DC. The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Research. 35: W455-9. PMID 17576682 DOI: 10.1093/Nar/Gkm400  0.756
2006 Parthasarathi L, Devocelle M, Søndergaard C, Baran I, O'Dushlaine CT, Davey NE, Edwards RJ, Moran N, Kenny D, Shields DC. Absolute net charge and the biological activity of oligopeptides. Journal of Chemical Information and Modeling. 46: 2183-90. PMID 16995748 DOI: 10.1021/Ci0600760  0.606
2006 Davey NE, Shields DC, Edwards RJ. SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Research. 34: 3546-54. PMID 16855291 DOI: 10.1093/Nar/Gkl486  0.743
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