Publication List

1: 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 (Database issue):D508-516.
doi: 10.1093/nar/gks1226. PubMed PMID: 223203878.

2: 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:e56465.
doi: 10.1371/journal.pone.0056465. PubMed PMID: 23418572.

3: Pajkos M, Mészáros B, Simon I, Dosztányi Z.
Is there a biological cost of protein disorder? Analysis of cancer-associated mutations.
Mol Biosyst. 2012;8:296-307.
doi: 10.1039/c1mb05246b. PubMed PMID: 21918772.

4: 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:e46829.
doi: 10.1371/journal.pone.0046829. PubMed PMID: 23056474.

5: 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;7:e1002118.
doi: 10.1371/journal.pcbi.1002118. PubMed PMID: 21814507.

6: Mészáros B, Simon I, Dosztányi Z.
The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins.
Phys Biol. 2011;8:035003.
doi: 10.1088/1478-3975/8/3/035003. PubMed PMID: 21572179

7: Dosztányi Z, Mészáros B, Simon I.
Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins.
Brief Bioinform. 2010;11:225-43.
doi: 10.1093/bib/bbp061. PubMed PMID: 20007729.

8: Dosztányi Z, Mészáros B, Simon I.
ANCHOR: web server for predicting protein binding regions in disordered proteins.
Bioinformatics. 2009 15;25:2745-6.
doi: 10.1093/bioinformatics/btp518. PubMed PMID: 19717576.

9: Mészáros B, Simon I, Dosztányi Z.
Prediction of protein binding regions in disordered proteins.
PLoS Comput Biol. 2009;5:e1000376.
doi: 10.1371/journal.pcbi.1000376. PubMed PMID: 19412530.

10: Csosz E, Bagossi P, Nagy Z, Dosztanyi 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. PubMed PMID: 18761350.

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

12: Mészáros B, Tompa P, Simon I, Dosztányi Z.
Molecular principles of the interactions of disordered proteins.
J Mol Biol. 2007 ;372:549-561.
PubMed PMID: 17681540.

13: Csizmók V, Dosztányi Z, Simon I, Tompa P.
Towards proteomic approaches for the identification of structural disorder.
Curr Protein Pept Sci. 2007;8:173-179. Review.
PubMed PMID: 17430198.

14: Dosztányi Z, Sándor M, Tompa P, Simon I.
Prediction of protein disorder at the domain level.
Curr Protein Pept Sci. 2007;8:161-171. Review.
PubMed PMID: 17430197.

15: 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.
PubMed PMID: 17081050.

16: Tompa P, Dosztanyi Z, Simon I.
Prevalent structural disorder in E. coli and S. cerevisiae proteomes.
J Proteome Res. 2006 Aug;5(8):1996-2000.
PubMed PMID: 16889422.

17: 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 ;21:3433-3434.
PubMed PMID: 15955779.

18: 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;347:827-839.
PubMed PMID: 15769473.

19: Tusnády GE, Dosztányi Z, Simon I.
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates.
Bioinformatics. 2005 Apr 1;21:1276-7.
PubMed PMID: 15539454.

20: 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;346:1229-41.
PubMed PMID: 15713477.

21: Tusnády GE, Dosztányi Z, Simon I.
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank.
Nucleic Acids Res. 2005 1;33(Database issue):D275-D278.
PubMed PMID: 15608195.

22: Tusnády GE, Dosztányi Z, Simon I.
Transmembrane proteins in the Protein Data Bank: identification and classification.
Bioinformatics. 2004 ;20:2964-2972.
PubMed PMID: 15180935.

23: 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 ;44:347-51. Review.
PubMed PMID: 15032510.

24: Dosztányi Z, Magyar C, Tusnády GE, Cserzo M, Fiser A, Simon I.
Servers for sequence-structure relationship analysis and prediction.
Nucleic Acids Res. 2003 ;31:3359-33363.
PubMed PMID: 12824327.

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

26: Dosztányi Z, Torda AE.
Amino acid similarity matrices based on force fields.
Bioinformatics. 2001 Aug;17:686-699.
PubMed PMID: 11524370.

27: Simon A, Dosztányi Zs, Rajnavölgyi E, Simon I.
Function-related regulation of the stability of MHC proteins.
Biophys J. 2000 79:2305-13.
PubMed PMID: 11053110.

28: 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 ;12:281-293.
PubMed PMID: 10700463.

29: Dosztányi Z, Fiser A, Simon I.
Stabilization centers in proteins: identification, characterization and predictions.
J Mol Biol. 1997;272:597-612.
PubMed PMID: 9325115.

30: 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 ;13:297-301.
PubMed PMID: 9183535.

31: Gugolya Z, Dosztányi Z, Simon I.
Interresidue interactions in protein classes.
Proteins. 1997;27:360-366.
PubMed PMID: 9094738.