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Items: 29

1.

Covering complete proteomes with X-ray structures: a current snapshot.

Mizianty MJ, Fan X, Yan J, Chalmers E, Woloschuk C, Joachimiak A, Kurgan L.

Acta Crystallogr D Biol Crystallogr. 2014 Nov;70(Pt 11):2781-93. doi: 10.1107/S1399004714019427. Epub 2014 Oct 23.

2.

Human structural proteome-wide characterization of Cyclosporine A targets.

Hu G, Wang K, Groenendyk J, Barakat K, Mizianty MJ, Ruan J, Michalak M, Kurgan L.

Bioinformatics. 2014 Dec 15;30(24):3561-6. doi: 10.1093/bioinformatics/btu581. Epub 2014 Aug 28.

3.

Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life.

Peng Z, Yan J, Fan X, Mizianty MJ, Xue B, Wang K, Hu G, Uversky VN, Kurgan L.

Cell Mol Life Sci. 2015 Jan;72(1):137-51. doi: 10.1007/s00018-014-1661-9. Epub 2014 Jun 18.

PMID:
24939692
4.

Interplay between the oxidoreductase PDIA6 and microRNA-322 controls the response to disrupted endoplasmic reticulum calcium homeostasis.

Groenendyk J, Peng Z, Dudek E, Fan X, Mizianty MJ, Dufey E, Urra H, Sepulveda D, Rojas-Rivera D, Lim Y, Kim DH, Baretta K, Srikanth S, Gwack Y, Ahnn J, Kaufman RJ, Lee SK, Hetz C, Kurgan L, Michalak M.

Sci Signal. 2014 Jun 10;7(329):ra54. doi: 10.1126/scisignal.2004983.

5.

Prediction of intrinsic disorder in proteins using MFDp2.

Mizianty MJ, Uversky V, Kurgan L.

Methods Mol Biol. 2014;1137:147-62. doi: 10.1007/978-1-4939-0366-5_11.

PMID:
24573480
6.

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
7.

Genome-scale prediction of proteins with long intrinsically disordered regions.

Peng Z, Mizianty MJ, Kurgan L.

Proteins. 2014 Jan;82(1):145-58. doi: 10.1002/prot.24348. Epub 2013 Sep 17.

PMID:
23798504
8.

RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale.

Yan J, Mizianty MJ, Filipow PL, Uversky VN, Kurgan L.

Biochim Biophys Acta. 2013 Aug;1834(8):1671-80. doi: 10.1016/j.bbapap.2013.05.022. Epub 2013 Jun 1.

PMID:
23732563
9.

Prediction and characterization of cyclic proteins from sequences in three domains of life.

Kedarisetti P, Mizianty MJ, Kaas Q, Craik DJ, Kurgan L.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt B):181-90. doi: 10.1016/j.bbapap.2013.05.002. Epub 2013 May 10.

PMID:
23669569
10.

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.

11.

MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles.

Mizianty MJ, Peng Z, Kurgan L.

Intrinsically Disord Proteins. 2013 Apr 1;1(1):e24428. doi: 10.4161/idp.24428. eCollection 2013 Jan-Dec.

12.

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.

13.

Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions.

Hu G, Gao J, Wang K, Mizianty MJ, Ruan J, Kurgan L.

Structure. 2012 Nov 7;20(11):1815-22. doi: 10.1016/j.str.2012.09.011.

14.

Monocytes from patients with osteoarthritis display increased osteoclastogenesis and bone resorption: the In Vitro Osteoclast Differentiation in Arthritis study.

Durand M, Komarova SV, Bhargava A, Trebec-Reynolds DP, Li K, Fiorino C, Maria O, Nabavi N, Manolson MF, Harrison RE, Dixon SJ, Sims SM, Mizianty MJ, Kurgan L, Haroun S, Boire G, de Fatima Lucena-Fernandes M, de Brum-Fernandes AJ.

Arthritis Rheum. 2013 Jan;65(1):148-58. doi: 10.1002/art.37722.

15.

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.

16.

More than just tails: intrinsic disorder in histone proteins.

Peng Z, Mizianty MJ, Xue B, Kurgan L, Uversky VN.

Mol Biosyst. 2012 Jul 6;8(7):1886-901. doi: 10.1039/c2mb25102g. Epub 2012 Apr 27.

PMID:
22543956
17.

ATPsite: sequence-based prediction of ATP-binding residues.

Chen K, Mizianty MJ, Kurgan L.

Proteome Sci. 2011 Oct 14;9 Suppl 1:S4. doi: 10.1186/1477-5956-9-S1-S4.

18.

Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors.

Chen K, Mizianty MJ, Kurgan L.

Bioinformatics. 2012 Feb 1;28(3):331-41. doi: 10.1093/bioinformatics/btr657. Epub 2011 Nov 29.

PMID:
22130595
19.

Protein intrinsic disorder as a flexible armor and a weapon of HIV-1.

Xue B, Mizianty MJ, Kurgan L, Uversky VN.

Cell Mol Life Sci. 2012 Apr;69(8):1211-59. doi: 10.1007/s00018-011-0859-3. Epub 2011 Oct 28. Review.

PMID:
22033837
20.
21.

Sequence-based prediction of protein crystallization, purification and production propensity.

Mizianty MJ, Kurgan L.

Bioinformatics. 2011 Jul 1;27(13):i24-33. doi: 10.1093/bioinformatics/btr229.

22.

In-silico prediction of disorder content using hybrid sequence representation.

Mizianty MJ, Zhang T, Xue B, Zhou Y, Dunker AK, Uversky VN, Kurgan L.

BMC Bioinformatics. 2011 Jun 17;12:245. doi: 10.1186/1471-2105-12-245.

23.

A critical comparative assessment of predictions of protein-binding sites for biologically relevant organic compounds.

Chen K, Mizianty MJ, Gao J, Kurgan L.

Structure. 2011 May 11;19(5):613-21. doi: 10.1016/j.str.2011.02.015.

24.

Improved sequence-based prediction of strand residues.

Kedarisetti KD, Mizianty MJ, Dick S, Kurgan L.

J Bioinform Comput Biol. 2011 Feb;9(1):67-89.

PMID:
21328707
25.

Critical assessment of high-throughput standalone methods for secondary structure prediction.

Zhang H, Zhang T, Chen K, Kedarisetti KD, Mizianty MJ, Bao Q, Stach W, Kurgan L.

Brief Bioinform. 2011 Nov;12(6):672-88. doi: 10.1093/bib/bbq088. Epub 2011 Jan 20.

PMID:
21252072
26.
27.

Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources.

Mizianty MJ, Stach W, Chen K, Kedarisetti KD, Disfani FM, Kurgan L.

Bioinformatics. 2010 Sep 15;26(18):i489-96. doi: 10.1093/bioinformatics/btq373.

28.

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences.

Mizianty MJ, Kurgan L.

BMC Bioinformatics. 2009 Dec 13;10:414. doi: 10.1186/1471-2105-10-414.

29.

Meta prediction of protein crystallization propensity.

Mizianty MJ, Kurgan L.

Biochem Biophys Res Commun. 2009 Dec 4;390(1):10-5. doi: 10.1016/j.bbrc.2009.09.036. Epub 2009 Sep 13.

PMID:
19755114

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