PUBLICATION LIST

ZSUZSANNA DOSZTÁNYI

2024

1: Aspromonte MC, Nugnes MV, Quaglia F, Bouharoua A, … Dosztányi Z, ... Tosatto SCE, Piovesan D. DisProt in 2024: improving function annotation of intrinsically disordered proteins. Nucleic Acids Res. 2024 Jan 5;52(D1):D434-D441. Doi: 10.1093/nar/gkad928. PMID: 37904585; PMCID: PMC10767923.

2: Pajkos M, Erdős G, Dosztányi Z. The Origin of Discrepancies between Predictions and Annotations in Intrinsically Disordered Proteins. Biomolecules. 2023 Sep 25;13(10):1442. doi: 10.3390/biom13101442. PMID: 37892124; PMCID: PMC10604070.

3: Kurgan L, Hu G, Wang K, Ghadermarzi S, Zhao B, Malhis N, Erdős G, Gsponer J, Uversky VN, Dosztányi Z. Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins. Nat Protoc. 2023 Nov;18(11):3157-3172. doi:

10.1038/s41596-023-00876-x. Epub 2023 Sep 22. PMID: 37740110.

4: 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. Minimum information guidelines for experiments structurally characterizing intrinsically

disordered protein regions. Nat Methods. 2023 Sep;20(9):1291-1303. Doi: 10.1038/s41592-023-01915-x. Epub 2023 Jul 3. PMID: 37400558.

5: Del Conte A, Bouhraoua A, Mehdiabadi M, Clementel D, Monzon AM, ...Dosztányi Z, ... Tosatto SCE, Piovesan D. CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 2023 Jul 5;51(W1):W62-W69. doi: 10.1093/nar/gkad430. PMID: 37246642; PMCID: PMC10320102.

6: Martínez-Pérez E, Pajkos M, Tosatto SCE, Gibson TJ, Dosztányi Z, Marino-Buslje C. Pipeline for transferring annotations between proteins beyond globular domains. Protein Sci. 2023 Jul;32(7):e4655. doi: 10.1002/pro.4655. PMID: 37167423; PMCID: PMC10278204.

7: Ashton AW, Dhanjal HK, Rossner B, Mahmood H, Patel VI, Nadim M, Lota M, Shahid F, Li Z, Joyce D, Pajkos M, Dosztányi Z, Jiao X, Pestell RG. Acetylation of nuclear receptors in health and disease: an update. FEBS J. 2024 Jan;291(2):217-236. doi: 10.1111/febs.16695. Epub 2022 Dec 19. PMID: 36471658.

8: Deutsch N, Pajkos M, Erdős G, Dosztányi Z. DisCanVis: Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins. Protein Sci. 2023 Jan;32(1):e4522. doi: 10.1002/pro.4522. PMID: 36452990; PMCID: PMC9793970.

9: Kastano K, Mier P, Dosztányi Z, Promponas VJ, Andrade-Navarro MA. Functional Tuning of Intrinsically Disordered Regions in Human Proteins by Composition Bias. Biomolecules. 2022 Oct 15;12(10):1486. doi: 10.3390/biom12101486. PMID: 36291695; PMCID: PMC9599065.

10: Szaniszló T, Fülöp M, Pajkos M, Erdős G, Kovács RÁ, Vadászi H, Kardos J, Dosztányi Z. The interaction between LC8 and LCA5 reveals a novel oligomerization function of LC8 in the ciliary-centrosome system. Sci Rep. 2022 Sep 16;12(1):15623. doi: 10.1038/s41598-022-19454-4. PMID: 36114230; PMCID: PMC9481538.

11: 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, Paris G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res. 2022 Jan 7;50(D1):D480-D487. doi: 10.1093/nar/gkab1082. PMID: 34850135; PMCID: PMC8728214.

12: Pajkos M, Dosztányi Z. Functions of intrinsically disordered proteins through evolutionary lenses. Prog Mol Biol Transl Sci. 2021;183:45-74. doi: 10.1016/bs.pmbts.2021.06.017. Epub 2021 Jul 29. PMID: 34656334.

13: Erdős G, Pajkos M, Dosztányi Z. IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation. Nucleic Acids Res. 2021 Jul 2;49(W1):W297-W303. Doi: 10.1093/nar/gkab408. PMID: 34048569; PMCID: PMC8262696.

14: Necci M, Piovesan D; ...Dosztányi Z, ... DisProt Curators; Tosatto SCE. Critical assessment of protein intrinsic disorder prediction. Nat Methods. 2021 May;18(5):472-481. doi: 10.1038/s41592-021-01117-3. Epub 2021 Apr 19. PMID: 33875885; PMCID: PMC8105172.

15: Mészáros B, Hajdu-Soltész B, Zeke A, Dosztányi Z. Mutations of Intrinsically Disordered Protein Regions Can Drive Cancer but Lack Therapeutic Strategies. Biomolecules. 2021 Mar 4;11(3):381. doi: 10.3390/biom11030381. PMID: 33806614; PMCID: PMC8000335.

16: Necci M, Piovesan D, Clementel D, Dosztányi Z, Tosatto SCE. MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins. Bioinformatics. 2021 Apr 1;36(22-23):5533-5534. doi: 10.1093/bioinformatics/btaa1045. PMID: 33325498.

17: 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 Res. 2021 Jan 8;49(D1):D361-D367. doi: 10.1093/nar/gkaa1058. PMID: 33237329; PMCID: PMC7779018.

18: Csizmadia G, Erdős G, Tordai H, Padányi R, Tosatto S, Dosztányi Z, Hegedűs T. The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. Nucleic Acids Res. 2021 Jan 8;49(D1):D355-D360. Doi: 10.1093/nar/gkaa954. PMID: 33119751; PMCID: PMC7778998.

19: Kastano K, Erdős G, Mier P, Alanis-Lobato G, Promponas VJ, Dosztányi Z, Andrade-Navarro MA. Evolutionary Study of Disorder in Protein Sequences. Biomolecules. 2020 Oct 6;10(10):1413. doi: 10.3390/biom10101413. PMID: 33036302; PMCID: PMC7650552.

20: Pajkos M, Zeke A, Dosztányi Z. Ancient Evolutionary Origin of Intrinsically Disordered Cancer Risk Regions. Biomolecules. 2020 Jul 28;10(8):1115. doi: 10.3390/biom10081115. PMID: 32731489; PMCID: PMC7465906.

21: Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro MA, Hancock JM, Dosztányi Z, Paladin L, Necci M, Piovesan D, Tosatto SCE, Promponas VJ, Grynberg M, Gruca A. PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. Nucleic Acids Res. 2020 Jul 2;48(W1):W77-W84. doi: 10.1093/nar/gkaa339. PMID: 32421769; PMCID: PMC7319588.

22: Erdős G, Dosztányi Z. Analyzing Protein Disorder with IUPred2A. Curr Protoc Bioinformatics. 2020 Jun;70(1):e99. doi: 10.1002/cpbi.99. PMID: 32237272.

23: Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztányi 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. An intrinsically disordered proteins community for ELIXIR. F1000Res. 2019 Oct 15;8:ELIXIR-1753. Doi: 10.12688/f1000research.20136.1. PMID: 31824649; PMCID: PMC6880265.

24: 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. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 2020 Jan

8;48(D1):D269-D276. doi: 10.1093/nar/gkz975. PMID: 31713636; PMCID: PMC7145575.

25: Mészáros B, Erdős G, Szabó B, Schád É, Tantos Á, Abukhairan R, Horváth T, Murvai N, Kovács OP, Kovács M, Tosatto SCE, Tompa P, Dosztányi Z, Pancsa R. PhaSePro: the database of proteins driving liquid-liquid phase separation. Nucleic Acids Res. 2020 Jan 8;48(D1):D360-D367. doi: 10.1093/nar/gkz848. PMID: 31612960; PMCID: PMC7145634.

26: Mészáros B, Dobson L, Fichó E, Tusnády GE, Dosztányi Z, Simon I. Sequential, Structural and Functional Properties of Protein Complexes Are Defined by How Folding and Binding Intertwine. J Mol Biol. 2019 Nov 8;431(22):4408-4428. doi: 10.1016/j.jmb.2019.07.034. Epub 2019 Aug 12. PMID: 31415767.

27: Mier P, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis CA, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztányi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform. 2020 Mar 23;21(2):458-472. doi: 10.1093/bib/bbz007. PMID: 30698641; PMCID:

PMC7299295.

28: Erdős G, Mészáros B, Reichmann D, Dosztányi Z. Large-Scale Analysis of Redox-Sensitive Conditionally Disordered Protein Regions Reveals Their Widespread Nature and Key Roles in High-Level Eukaryotic Processes. Proteomics. 2019 Mar;19(6):e1800070. doi: 10.1002/pmic.201800070. Epub 2019 Jan 28. PMID: 30628183.

29: Mészáros B, Erdos G, Dosztányi Z. IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res. 2018 Jul 2;46(W1):W329-W337. doi: 10.1093/nar/gky384. PMID: 29860432; PMCID: PMC6030935.

30: Schad E, Fichó E, Pancsa R, Simon I, Dosztányi Z, Mészáros B. DIBS: a repository of disordered binding sites mediating interactions with ordered proteins. Bioinformatics. 2018 Feb 1;34(3):535-537. doi: 10.1093/bioinformatics/btx640. PMID: 29385418; PMCID: PMC5860366.

31: Erdős G, Szaniszló T, Pajkos M, Hajdu-Soltész B, Kiss B, Pál G, Nyitray L, Dosztányi Z. Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway. PLoS Comput Biol. 2017 Dec 14;13(12):e1005885. doi: 10.1371/journal.pcbi.1005885. PMID: 29240760; PMCID: PMC5746249.

32: 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, Vranken WF, Tosatto SCE. MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. Nucleic Acids Res. 2018 Jan 4;46(D1):D471-D476. doi: 10.1093/nar/gkx1071. PMID: 29136219; PMCID: PMC5753340.

33: Dosztányi Z. Prediction of protein disorder based on IUPred. Protein Sci. 2018 Jan;27(1):331-340. doi: 10.1002/pro.3334. Epub 2017 Nov 16. PMID: 29076577; PMCID: PMC5734386.

34: Necci M, Piovesan D, Dosztányi Z, Tompa P, Tosatto SCE. A comprehensive assessment of long intrinsic protein disorder from the DisProt database. Bioinformatics. 2018 Feb 1;34(3):445-452. doi: 10.1093/bioinformatics/btx590. PMID: 28968848.

35: Necci M, Piovesan D, Dosztányi Z, Tosatto SCE. MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. Bioinformatics. 2017 May 1;33(9):1402-1404. doi: 10.1093/bioinformatics/btx015. PMID: 28453683.

36: Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztányi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M. Simultaneous quantification of protein order and disorder. Nat Chem Biol. 2017 Mar 22;13(4):339-342. doi: 10.1038/nchembio.2331. PMID: 28328918.

37: Mészáros B, Kumar M, Gibson TJ, Uyar B, Dosztányi Z. Degrons in cancer. Sci Signal. 2017 Mar 14;10(470):eaak9982. doi: 10.1126/scisignal.aak9982. PMID: 28292960.

38: 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. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. Erratum for: Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. PMID: 27965415; PMCID: PMC5210598.

39: Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH,

Xenarios I, Yeh LS, Young SY, Mitchell AL. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29. PMID: 27899635; PMCID: PMC5210578.

40: 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. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 2017 Jan 4;45(D1):D219-D227. doi: 10.1093/nar/gkw1056. Epub 2016 Nov 28. Erratum in: Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. PMID: 27899601; PMCID: PMC5210544.

41: Mészáros B, Zeke A, Reményi A, Simon I, Dosztányi Z. Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development. Biol Direct. 2016 May 5;11:23. doi: 10.1186/s13062-016-0125-6. PMID: 27150584; PMCID: PMC4858844.

42: Zeke A, Bastys T, Alexa A, Garai Á, Mészáros B, Kirsch K, Dosztányi Z, Kalinina OV, Reményi A. Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases. Mol Syst Biol. 2015 Nov 3;11(11):837. doi: 10.15252/msb.20156269. PMID: 26538579; PMCID: PMC4670726.

43: Punta M, Simon I, Dosztányi Z. Prediction and analysis of intrinsically disordered proteins. Methods Mol Biol. 2015;1261:35-59. doi: 10.1007/978-1-4939-2230-7_3. PMID: 25502193.

44: Dunker AK, Babu MM, Barbar E, Blackledge M, Bondos SE, Dosztányi Z, Dyson HJ, Forman-Kay J, Fuxreiter M, Gsponer J, Han KH, Jones DT, Longhi S, Metallo SJ, Nishikawa K, Nussinov R, Obradovic Z, Pappu RV, Rost B, Selenko P, Subramaniam V, Sussman JL, Tompa P, Uversky VN. What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically

disordered. Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24157. Doi: 10.4161/idp.24157. PMID: 28516007; PMCID: PMC5424803.

45: Hayward DC, Dosztányi Z, Clark-Walker GD. The N-terminal intrinsically disordered domain of Mgm101p is localized to the mitochondrial nucleoid. PloS One. 2013;8(2):e56465. doi: 10.1371/journal.pone.0056465. Epub 2013 Feb 13. PMID: 23418572; PMCID: PMC3572067.

46: Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, Dunker AK, Gough J. D²P²: database of disordered protein predictions. Nucleic Acids Res. 2013 Jan;41(Database issue):D508-16. doi: 10.1093/nar/gks1226. Epub 2012 Nov 29. PMID: 23203878; PMCID: PMC3531159.

47: Mészáros B, Dosztányi Z, Simon I. Disordered binding regions and linear motifs--bridging the gap between two models of molecular recognition. PLoS One. 2012;7(10):e46829. doi: 10.1371/journal.pone.0046829. Epub 2012 Oct 3. PMID: 23056474; PMCID: PMC3463566.

48: Pajkos M, Mészáros B, Simon I, Dosztányi Z. Is there a biological cost of protein disorder? Analysis of cancer-associated mutations. Mol Biosyst. 2012 Jan;8(1):296-307. doi: 10.1039/c1mb05246b. Epub 2011 Sep 14. PMID: 21918772.

49: Mészáros B, Tóth J, Vértessy BG, Dosztányi Z, Simon I. Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis. PLoS Comput Biol. 2011 Jul;7(7):e1002118. Doi: 10.1371/journal.pcbi.1002118. Epub 2011 Jul 21. PMID: 21814507; PMCID:

PMC3140968.

50: Mészáros B, Simon I, Dosztányi Z. The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins. Phys Biol. 2011 Jun;8(3):035003. doi: 10.1088/1478-3975/8/3/035003. Epub 2011 May 13. PMID: 21572179.

51: Dosztányi Z, Mészáros B, Simon I. Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. Brief Bioinform. 2010 Mar;11(2):225-43. doi: 10.1093/bib/bbp061. Epub 2009 Dec 10. PMID: 20007729.

52: Dosztányi Z, Mészáros B, Simon I. ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics. 2009 Oct 15;25(20):2745-6. doi: 10.1093/bioinformatics/btp518. Epub 2009 Aug 28. PMID: 19717576; PMCID: PMC2759549.

53: Mészáros B, Simon I, Dosztányi Z. Prediction of protein binding regions in disordered proteins. PLoS Comput Biol. 2009 May;5(5):e1000376. Doi: 10.1371/journal.pcbi.1000376. Epub 2009 May 1. PMID: 19412530; PMCID: PMC2671142.

54: Csosz E, Bagossi P, Nagy Z, Dosztányi Z, Simon I, Fesus L. Substrate preference of transglutaminase 2 revealed by logistic regression analysis and intrinsic disorder examination. J Mol Biol. 2008 Nov 7;383(2):390-402. doi: 10.1016/j.jmb.2008.08.026. Epub 2008 Aug 22. PMID: 18761350.

55: Dosztányi Z, Tompa P. Prediction of protein disorder. Methods Mol Biol. 2008;426:103-15. doi: 10.1007/978-1-60327-058-8_6. PMID: 18542859.

56: Mészáros B, Tompa P, Simon I, Dosztányi Z. Molecular principles of the interactions of disordered proteins. J Mol Biol. 2007 Sep 14;372(2):549-61. doi: 10.1016/j.jmb.2007.07.004. Epub 2007 Jul 12. PMID: 17681540.

57: Csizmók V, Dosztányi Z, Simon I, Tompa P. Towards proteomic approaches for the identification of structural disorder. Curr Protein Pept Sci. 2007 Apr;8(2):173-9. doi: 10.2174/138920307780363479. PMID: 17430198.

58: Dosztányi Z, Sándor M, Tompa P, Simon I. Prediction of protein disorder at the domain level. Curr Protein Pept Sci. 2007 Apr;8(2):161-71. Doi: 10.2174/138920307780363406. PMID: 17430197.

59: Dosztányi Z, Chen J, Dunker AK, Simon I, Tompa P. Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res. 2006 Nov;5(11):2985-95. doi: 10.1021/pr060171o. PMID: 17081050.

60: Tompa P, Dosztányi Z, Simon I. Prevalent structural disorder in E. coli and S. cerevisiae proteomes. J Proteome Res. 2006 Aug;5(8):1996-2000. Doi: 10.1021/pr0600881. PMID: 16889422.

61: Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics. 2005 Aug 15;21(16):3433-4. doi: 10.1093/bioinformatics/bti541. Epub 2005 Jun 14. PMID: 15955779.

62: Dosztányi Z, Csizmók V, Tompa P, Simon I. The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol. 2005 Apr 8;347(4):827-39. doi: 10.1016/j.jmb.2005.01.071. PMID: 15769473.

63: Robinson A, Wu PS, Harrop SJ, Schaeffer PM, Dosztányi Z, Gillings MR, Holmes AJ, Nevalainen KM, Stokes HW, Otting G, Dixon NE, Curmi PM, Mabbutt BC. Integron-associated mobile gene cassettes code for folded proteins: the structure of Bal32a, a new member of the adaptable alpha+beta barrel family. J Mol Biol. 2005 Mar 11;346(5):1229-41. doi: 10.1016/j.jmb.2004.12.035. Epub 2004

Dec 31. PMID: 15713477.

64: Tusnády GE, Dosztányi Z, Simon I. PDB_TM: selection and membranelocalization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D275-8. doi: 10.1093/nar/gki002. PMID: 15608195; PMCID: PMC539956.

65: Tusnády GE, Dosztányi Z, Simon I. TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics. 2005 Apr 1;21(7):1276-7. doi: 10.1093/bioinformatics/bti121. Epub 2004 Nov 11. PMID: 15539454.

66: Tusnády GE, Dosztányi Z, Simon I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics. 2004 Nov 22;20(17):2964-72. doi: 10.1093/bioinformatics/bth340. Epub 2004 Jun 4. PMID: 15180935.

67: Tüdos E, Fiser A, Simon A, Dosztányi Z, Fuxreiter M, Magyar C, Simon I. Noncovalent cross-links in context with other structural and functional elements of proteins. J Chem Inf Comput Sci. 2004 Mar-Apr;44(2):347-51. Doi: 10.1021/ci030409i. PMID: 15032510.

68: Dosztányi Z, Magyar C, Tusnády GE, Cserzo M, Fiser A, Simon I. Servers for sequence-structure relationship analysis and prediction. Nucleic Acids Res. 2003 Jul 1;31(13):3359-63. doi: 10.1093/nar/gkg589. PMID: 12824327; PMCID: PMC168995.

69: Dosztányi Z, Magyar C, Tusnády G, Simon I. SCide: identification of stabilization centers in proteins. Bioinformatics. 2003 May 1;19(7):899-900. doi: 10.1093/bioinformatics/btg110. PMID: 12724305.

70: Dosztányi Z, Torda AE. Amino acid similarity matrices based on force fields. Bioinformatics. 2001 Aug;17(8):686-99. doi: 10.1093/bioinformatics/17.8.686. PMID: 11524370.

71: Simon A, Dosztányi Z, Rajnavölgyi E, Simon I. Function-related regulation of the stability of MHC proteins. Biophys J. 2000 Nov;79(5):2305-13. Doi: 10.1016/S0006-3495(00)76476-9. PMID: 11053110; PMCID: PMC1301118.

72: Rajnavölgyi E, Nagy N, Thuresson B, Dosztányi Z, Simon A, Simon I, Karr RW, Ernberg I, Klein E, Falk KI. A repetitive sequence of Epstein-Barr virus nuclear antigen 6 comprises overlapping T cell epitopes which induce HLA-DR-restricted CD4(+) T lymphocytes. Int Immunol. 2000 Mar;12(3):281-93. Doi: 10.1093/intimm/12.3.281. PMID: 10700463.

73: Dosztányi Z, Fiser A, Simon I. Stabilization centers in proteins: identification, characterization and predictions. J Mol Biol. 1997 Oct 3;272(4):597-612. doi: 10.1006/jmbi.1997.1242. PMID: 9325115.

74: Fiser A, Dosztányi Z, Simon I. The role of long-range interactions in defining the secondary structure of proteins is overestimated. Comput Appl Biosci. 1997 Jun;13(3):297-301. doi: 10.1093/bioinformatics/13.3.297. PMID: 9183535.

75: Gugolya Z, Dosztányi Z, Simon I. Interresidue interactions in protein classes. Proteins. 1997 Mar;27(3):360-6. PMID: 9094738.