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Page 1
A structural biology community assessment of AlphaFold2 applications.
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, Dunham AS, Burke D, Borkakoti N, Velankar S, Frost A, Basquin J, Lindorff-Larsen K, Bateman A, Kajava AV, Valencia A, Ovchinnikov S, Durairaj J, Ascher DB, Thornton JM, Davey NE, Stein A, Elofsson A, Croll TI, Beltrao P. Akdel M, et al. Among authors: davey ne. Nat Struct Mol Biol. 2022 Nov;29(11):1056-1067. doi: 10.1038/s41594-022-00849-w. Epub 2022 Nov 7. Nat Struct Mol Biol. 2022. PMID: 36344848 Free PMC article.
DisProt 7.0: a major update of the database of disordered proteins.
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, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. Piovesan D, et al. Among authors: davey ne. Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899601 Free PMC article.
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. Hatos A, et al. Among authors: davey ne. Nucleic Acids Res. 2020 Jan 8;48(D1):D269-D276. doi: 10.1093/nar/gkz975. Nucleic Acids Res. 2020. PMID: 31713636 Free PMC article.
An intrinsically disordered proteins community for ELIXIR.
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, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. Davey NE, et al. F1000Res. 2019 Oct 15;8:ELIXIR-1753. doi: 10.12688/f1000research.20136.1. eCollection 2019. F1000Res. 2019. PMID: 31824649 Free PMC article.
Critical assessment of protein intrinsic disorder prediction.
Necci M, Piovesan D; CAID Predictors; DisProt Curators; Tosatto SCE. Necci M, et al. Nat Methods. 2021 May;18(5):472-481. doi: 10.1038/s41592-021-01117-3. Epub 2021 Apr 19. Nat Methods. 2021. PMID: 33875885 Free PMC article.
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation.
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, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. Quaglia F, et al. Among authors: davey ne. Nucleic Acids Res. 2022 Jan 7;50(D1):D480-D487. doi: 10.1093/nar/gkab1082. Nucleic Acids Res. 2022. PMID: 34850135 Free PMC article.
Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions.
Mészáros B, Hatos A, Palopoli N, Quaglia F, Salladini E, Van Roey K, Arthanari H, Dosztányi Z, Felli IC, Fischer PD, Hoch JC, Jeffries CM, Longhi S, Maiani E, Orchard S, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Pritisanac I, Tenorio L, Viennet T, Tompa P, Vranken W, Tosatto SCE, Davey NE. Mészáros B, et al. Among authors: davey ne. Nat Methods. 2023 Sep;20(9):1291-1303. doi: 10.1038/s41592-023-01915-x. Epub 2023 Jul 3. Nat Methods. 2023. PMID: 37400558 Review.
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. Gould CM, et al. Among authors: davey ne. Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016. Epub 2009 Nov 17. Nucleic Acids Res. 2010. PMID: 19920119 Free PMC article.
Motif switches: decision-making in cell regulation.
Van Roey K, Gibson TJ, Davey NE. Van Roey K, et al. Among authors: davey ne. Curr Opin Struct Biol. 2012 Jun;22(3):378-85. doi: 10.1016/j.sbi.2012.03.004. Epub 2012 Apr 3. Curr Opin Struct Biol. 2012. PMID: 22480932 Review.
89 results