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Items: 1 to 50 of 228

1.

Evolution of Protein Ductility in Duplicated Genes of Plants.

Yruela I, Contreras-Moreira B, Dunker AK, Niklas KJ.

Front Plant Sci. 2018 Aug 20;9:1216. doi: 10.3389/fpls.2018.01216. eCollection 2018.

2.

Regulating Protein Function by Delayed Folding.

Zhou J, Dunker AK.

Structure. 2018 May 1;26(5):679-681. doi: 10.1016/j.str.2018.04.011.

PMID:
29719237
3.

Intrinsically Disordered Proteins Link Alternative Splicing and Post-translational Modifications to Complex Cell Signaling and Regulation.

Zhou J, Zhao S, Dunker AK.

J Mol Biol. 2018 Aug 3;430(16):2342-2359. doi: 10.1016/j.jmb.2018.03.028. Epub 2018 Apr 4.

PMID:
29626537
4.

The evolutionary origins of cell type diversification and the role of intrinsically disordered proteins.

Niklas KJ, Dunker AK, Yruela I.

J Exp Bot. 2018 Mar 24;69(7):1437-1446. doi: 10.1093/jxb/erx493.

PMID:
29394379
5.

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions.

Saravanan KM, Dunker AK, Krishnaswamy S.

J Biomol Struct Dyn. 2017 Dec 27:1-14. doi: 10.1080/07391102.2017.1415822. [Epub ahead of print]

PMID:
29228892
6.

Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.

Faraggi E, Dunker AK, Sussman JL, Kloczkowski A.

J Biomol Struct Dyn. 2018 Jul;36(9):2331-2341. doi: 10.1080/07391102.2017.1352539. Epub 2017 Aug 8.

7.

Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity.

Yruela I, Oldfield CJ, Niklas KJ, Dunker AK.

Genome Biol Evol. 2017 May 1;9(5):1248-1265. doi: 10.1093/gbe/evx073.

8.

Simultaneous quantification of protein order and disorder.

Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztanyi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M.

Nat Chem Biol. 2017 Mar 22;13(4):339-342. doi: 10.1038/nchembio.2331. No abstract available.

PMID:
28328918
9.

Time, space, and disorder in the expanding proteome universe.

Minde DP, Dunker AK, Lilley KS.

Proteomics. 2017 Apr;17(7). doi: 10.1002/pmic.201600399. Epub 2017 Mar 20.

10.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1123-D1124. doi: 10.1093/nar/gkw1279. Epub 2016 Dec 13. No abstract available.

11.

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.

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.

12.

Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells.

Zhou A, Li M, He B, Feng W, Huang F, Xu B, Dunker AK, Balch C, Li B, Liu Y, Wang Y.

BMC Genomics. 2016 Aug 22;17 Suppl 7:509. doi: 10.1186/s12864-016-2898-5.

13.

Prostate-associated gene 4 (PAGE4), an intrinsically disordered cancer/testis antigen, is a novel therapeutic target for prostate cancer.

Kulkarni P, Dunker AK, Weninger K, Orban J.

Asian J Androl. 2016 Sep-Oct;18(5):695-703. doi: 10.4103/1008-682X.181818. Review.

14.

Correlating Flavivirus virulence and levels of intrinsic disorder in shell proteins: protective roles vs. immune evasion.

Goh GK, Dunker AK, Uversky VN.

Mol Biosyst. 2016 May 24;12(6):1881-91. doi: 10.1039/c6mb00228e.

PMID:
27102744
15.

Molecular recognition features (MoRFs) in three domains of life.

Yan J, Dunker AK, Uversky VN, Kurgan L.

Mol Biosyst. 2016 Mar;12(3):697-710. doi: 10.1039/c5mb00640f.

16.

Back to the Future: Nuclear Magnetic Resonance and Bioinformatics Studies on Intrinsically Disordered Proteins.

Dunker AK, Oldfield CJ.

Adv Exp Med Biol. 2015;870:1-34. doi: 10.1007/978-3-319-20164-1_1. Review.

PMID:
26387098
17.

Erratum to: Improving protein order-disorder classification using charge-hydropathy plots.

Huang F, Oldfield CJ, Xue B, Hsu WL, Meng J, Liu X, Shen L, Romero P, Uversky VN, Dunker AK.

BMC Bioinformatics. 2015 Jul 31;16:241. doi: 10.1186/s12859-015-0646-5. No abstract available.

18.

Detection of links between Ebola nucleocapsid and virulence using disorder analysis.

Goh GK, Dunker AK, Uversky VN.

Mol Biosyst. 2015 Aug;11(8):2337-44. doi: 10.1039/c5mb00240k.

PMID:
26086270
19.

Shell disorder, immune evasion and transmission behaviors among human and animal retroviruses.

Goh GK, Dunker AK, Uversky VN.

Mol Biosyst. 2015 Aug;11(8):2312-23. doi: 10.1039/c5mb00277j.

PMID:
26080321
20.

Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications.

Niklas KJ, Bondos SE, Dunker AK, Newman SA.

Front Cell Dev Biol. 2015 Feb 26;3:8. doi: 10.3389/fcell.2015.00008. eCollection 2015.

21.

Intrinsic disorder mediates hepatitis C virus core-host cell protein interactions.

Dolan PT, Roth AP, Xue B, Sun R, Dunker AK, Uversky VN, LaCount DJ.

Protein Sci. 2015 Feb;24(2):221-35. doi: 10.1002/pro.2608. Epub 2014 Dec 31.

22.

Intrinsically disordered proteins and multicellular organisms.

Dunker AK, Bondos SE, Huang F, Oldfield CJ.

Semin Cell Dev Biol. 2015 Jan;37:44-55. doi: 10.1016/j.semcdb.2014.09.025. Epub 2014 Oct 13. Review.

PMID:
25307499
23.

The structural and functional signatures of proteins that undergo multiple events of post-translational modification.

Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P.

Protein Sci. 2014 Aug;23(8):1077-93. doi: 10.1002/pro.2494. Epub 2014 Jun 11.

24.

Classification of intrinsically disordered regions and proteins.

van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM.

Chem Rev. 2014 Jul 9;114(13):6589-631. doi: 10.1021/cr400525m. Epub 2014 Apr 29. Review. No abstract available.

25.

Intrinsically disordered proteins and intrinsically disordered protein regions.

Oldfield CJ, Dunker AK.

Annu Rev Biochem. 2014;83:553-84. doi: 10.1146/annurev-biochem-072711-164947. Epub 2014 Mar 5. Review.

PMID:
24606139
26.

Order-disorder interface characterization reveals critical factors for disease and drug targets.

Kallenbach J, Hsu WL, Dunker AK, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:101. eCollection 2013.

PMID:
24303310
27.

Prediction of Intrinsic Disorder in MERS-CoV/HCoV-EMC Supports a High Oral-Fecal Transmission.

Goh GK, Dunker AK, Uversky V.

PLoS Curr. 2013 Nov 13;5. pii: ecurrents.outbreaks.22254b58675cdebc256dbe3c5aa6498b. doi: 10.1371/currents.outbreaks.22254b58675cdebc256dbe3c5aa6498b.

28.

pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins.

Varadi M, Kosol S, Lebrun P, Valentini E, Blackledge M, Dunker AK, Felli IC, Forman-Kay JD, Kriwacki RW, Pierattelli R, Sussman J, Svergun DI, Uversky VN, Vendruscolo M, Wishart D, Wright PE, Tompa P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D326-35. doi: 10.1093/nar/gkt960. Epub 2013 Oct 29.

29.

A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome.

Peng Z, Oldfield CJ, Xue B, Mizianty MJ, Dunker AK, Kurgan L, Uversky VN.

Cell Mol Life Sci. 2014 Apr;71(8):1477-504. doi: 10.1007/s00018-013-1446-6. Epub 2013 Aug 13.

PMID:
23942625
30.

Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing.

Bhat-Nakshatri P, Song EK, Collins NR, Uversky VN, Dunker AK, O'Malley BW, Geistlinger TR, Carroll JS, Brown M, Nakshatri H.

BMC Med Genomics. 2013 Jun 11;6:21. doi: 10.1186/1755-8794-6-21.

31.

Another disordered chameleon: the Micro-Exon Gene 14 protein from Schistosomiasis.

Dunker AK.

Biophys J. 2013 Jun 4;104(11):2326-8. doi: 10.1016/j.bpj.2013.04.018. No abstract available.

32.

Sequences and topology: disorder, modularity, and post/pre translation modification.

Gough J, Dunker AK.

Curr Opin Struct Biol. 2013 Jun;23(3):417-9. doi: 10.1016/j.sbi.2013.05.001. Epub 2013 May 28. No abstract available.

PMID:
23721748
33.

Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.

Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM.

Curr Opin Struct Biol. 2013 Jun;23(3):443-50. doi: 10.1016/j.sbi.2013.03.006. Epub 2013 May 22. Review.

PMID:
23706950
34.

Stochastic machines as a colocalization mechanism for scaffold protein function.

Xue B, Romero PR, Noutsou M, Maurice MM, Rüdiger SG, William AM Jr, Mizianty MJ, Kurgan L, Uversky VN, Dunker AK.

FEBS Lett. 2013 Jun 5;587(11):1587-91. doi: 10.1016/j.febslet.2013.04.006. Epub 2013 Apr 18.

35.

Distribution and cluster analysis of predicted intrinsically disordered protein Pfam domains.

Williams RW, Xue B, Uversky VN, Dunker AK.

Intrinsically Disord Proteins. 2013 Apr 1;1(1):e25724. doi: 10.4161/idp.25724. eCollection 2013 Jan-Dec.

36.

Functional fragments of disorder in outer membrane β barrel proteins.

Kurup K, Dunker AK, Krishnaswamy S.

Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24848. doi: 10.4161/idp.24848. eCollection 2013 Jan-Dec.

37.

The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins.

Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN.

Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24360. doi: 10.4161/idp.24360. eCollection 2013 Jan-Dec. Review.

38.

What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered.

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.

Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24157. doi: 10.4161/idp.24157. eCollection 2013 Jan-Dec. Review.

39.
40.

Intrinsically disordered regions of p53 family are highly diversified in evolution.

Xue B, Brown CJ, Dunker AK, Uversky VN.

Biochim Biophys Acta. 2013 Apr;1834(4):725-38. doi: 10.1016/j.bbapap.2013.01.012. Epub 2013 Jan 22.

41.

Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding.

Hsu WL, Oldfield CJ, Xue B, Meng J, Huang F, Romero P, Uversky VN, Dunker AK.

Protein Sci. 2013 Mar;22(3):258-73. doi: 10.1002/pro.2207. Epub 2013 Jan 27.

42.

Utilization of protein intrinsic disorder knowledge in structural proteomics.

Oldfield CJ, Xue B, Van YY, Ulrich EL, Markley JL, Dunker AK, Uversky VN.

Biochim Biophys Acta. 2013 Feb;1834(2):487-98. doi: 10.1016/j.bbapap.2012.12.003. Epub 2012 Dec 8.

43.

D²P²: database of disordered protein predictions.

Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, Dunker AK, Gough J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D508-16. doi: 10.1093/nar/gks1226. Epub 2012 Nov 29.

44.

An assignment of intrinsically disordered regions of proteins based on NMR structures.

Ota M, Koike R, Amemiya T, Tenno T, Romero PR, Hiroaki H, Dunker AK, Fukuchi S.

J Struct Biol. 2013 Jan;181(1):29-36. doi: 10.1016/j.jsb.2012.10.017. Epub 2012 Nov 7.

45.

Understanding Viral Transmission Behavior via Protein Intrinsic Disorder Prediction: Coronaviruses.

Goh GK, Dunker AK, Uversky VN.

J Pathog. 2012;2012:738590. doi: 10.1155/2012/738590. Epub 2012 Oct 14.

46.

Sweeping away protein aggregation with entropic bristles: intrinsically disordered protein fusions enhance soluble expression.

Santner AA, Croy CH, Vasanwala FH, Uversky VN, Van YY, Dunker AK.

Biochemistry. 2012 Sep 18;51(37):7250-62. doi: 10.1021/bi300653m. Epub 2012 Sep 5.

47.

Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life.

Xue B, Dunker AK, Uversky VN.

J Biomol Struct Dyn. 2012;30(2):137-49. doi: 10.1080/07391102.2012.675145.

PMID:
22702725
48.

MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins.

Disfani FM, Hsu WL, Mizianty MJ, Oldfield CJ, Xue B, Dunker AK, Uversky VN, Kurgan L.

Bioinformatics. 2012 Jun 15;28(12):i75-83. doi: 10.1093/bioinformatics/bts209.

49.

Proline rich motifs as drug targets in immune mediated disorders.

Srinivasan M, Dunker AK.

Int J Pept. 2012;2012:634769. doi: 10.1155/2012/634769. Epub 2012 May 16.

50.

High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative.

Johnson DE, Xue B, Sickmeier MD, Meng J, Cortese MS, Oldfield CJ, Le Gall T, Dunker AK, Uversky VN.

J Struct Biol. 2012 Oct;180(1):201-15. doi: 10.1016/j.jsb.2012.05.013. Epub 2012 May 29.

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