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For: Walsh I, Martin AJM, Di Domenico T, Tosatto SCE. ESpritz: accurate and fast prediction of protein disorder. ACTA ACUST UNITED AC 2011;28:503-9. [PMID: 22190692 DOI: 10.1093/bioinformatics/btr682] [Citation(s) in RCA: 387] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
351
Wu Z, Hu G, Yang J, Peng Z, Uversky VN, Kurgan L. In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces. FEBS Lett 2015;589:2561-9. [DOI: 10.1016/j.febslet.2015.08.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 07/31/2015] [Accepted: 08/03/2015] [Indexed: 11/28/2022]
352
Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies. Int J Mol Sci 2015;16:19040-54. [PMID: 26287166 PMCID: PMC4581285 DOI: 10.3390/ijms160819040] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/15/2015] [Accepted: 08/04/2015] [Indexed: 12/13/2022]  Open
353
Tusnády GE, Dobson L, Tompa P. Disordered regions in transmembrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015;1848:2839-48. [PMID: 26275590 DOI: 10.1016/j.bbamem.2015.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 11/18/2022]
354
Varadi M, Vranken W, Guharoy M, Tompa P. Computational approaches for inferring the functions of intrinsically disordered proteins. Front Mol Biosci 2015;2:45. [PMID: 26301226 PMCID: PMC4525029 DOI: 10.3389/fmolb.2015.00045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/21/2015] [Indexed: 01/09/2023]  Open
355
Minervini G, Quaglia F, Tosatto SCE. Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health. Biochimie 2015;116:114-24. [PMID: 26187473 DOI: 10.1016/j.biochi.2015.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/12/2015] [Indexed: 12/18/2022]
356
An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions. Int J Mol Sci 2015. [PMID: 26198229 PMCID: PMC4519904 DOI: 10.3390/ijms160715384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
357
Wang Z, Yang Q, Li T, Cong P. DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach. PLoS One 2015;10:e0128334. [PMID: 26090958 PMCID: PMC4474717 DOI: 10.1371/journal.pone.0128334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 04/26/2015] [Indexed: 11/21/2022]  Open
358
Identifying Similar Patterns of Structural Flexibility in Proteins by Disorder Prediction and Dynamic Programming. Int J Mol Sci 2015;16:13829-49. [PMID: 26086829 PMCID: PMC4490526 DOI: 10.3390/ijms160613829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/31/2022]  Open
359
Faust O, Bigman L, Friedler A. A role of disordered domains in regulating protein oligomerization and stability. Chem Commun (Camb) 2015;50:10797-800. [PMID: 25054624 DOI: 10.1039/c4cc03863k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
360
Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015;16:153. [PMID: 25968230 PMCID: PMC4427981 DOI: 10.1186/s12859-015-0592-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/23/2015] [Indexed: 12/03/2022]  Open
361
Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015. [PMID: 25968230 DOI: 10.1186/s12859‐015‐0592‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
362
Uversky VN. Unreported intrinsic disorder in proteins: Disorder emergency room. INTRINSICALLY DISORDERED PROTEINS 2015;3:e1010999. [PMID: 28232885 DOI: 10.1080/21690707.2015.1010999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/01/2014] [Accepted: 11/24/2014] [Indexed: 10/23/2022]
363
Chetty S, Bhakat S, Martin AJM, Soliman MES. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights. J Biomol Struct Dyn 2015;34:135-51. [PMID: 25671669 DOI: 10.1080/07391102.2015.1018326] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
364
Frege T, Uversky VN. Intrinsically disordered proteins in the nucleus of human cells. Biochem Biophys Rep 2015;1:33-51. [PMID: 29124132 PMCID: PMC5668563 DOI: 10.1016/j.bbrep.2015.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022]  Open
365
Intrinsically disordered proteins in cellular signalling and regulation. Nat Rev Mol Cell Biol 2015;16:18-29. [PMID: 25531225 DOI: 10.1038/nrm3920] [Citation(s) in RCA: 1736] [Impact Index Per Article: 173.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
366
Liu S, Cai X, Wu J, Cong Q, Chen X, Li T, Du F, Ren J, Wu YT, Grishin NV, Chen ZJ. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 2015;347:aaa2630. [PMID: 25636800 DOI: 10.1126/science.aaa2630] [Citation(s) in RCA: 1376] [Impact Index Per Article: 137.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
367
Singh GP. Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis. PeerJ 2015;3:e724. [PMID: 25648268 PMCID: PMC4304846 DOI: 10.7717/peerj.724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/21/2014] [Indexed: 01/28/2023]  Open
368
Punta M, Simon I, Dosztányi Z. Prediction and analysis of intrinsically disordered proteins. Methods Mol Biol 2015;1261:35-59. [PMID: 25502193 DOI: 10.1007/978-1-4939-2230-7_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
369
Peng Z, Yan J, Fan X, Mizianty MJ, Xue B, Wang K, Hu G, Uversky VN, Kurgan L. Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. Cell Mol Life Sci 2015;72:137-51. [PMID: 24939692 PMCID: PMC11113594 DOI: 10.1007/s00018-014-1661-9] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 02/02/2023]
370
Spencer M, Eickholt J, Cheng J. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:103-12. [PMID: 25750595 PMCID: PMC4348072 DOI: 10.1109/tcbb.2014.2343960] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
371
A critical evaluation of in silico methods for detection of membrane protein intrinsic disorder. Biophys J 2014;106:1638-49. [PMID: 24739163 DOI: 10.1016/j.bpj.2014.02.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/03/2014] [Accepted: 02/25/2014] [Indexed: 11/23/2022]  Open
372
Kumari B, Kumar R, Kumar M. Low complexity and disordered regions of proteins have different structural and amino acid preferences. MOLECULAR BIOSYSTEMS 2014;11:585-94. [PMID: 25468592 DOI: 10.1039/c4mb00425f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
373
Uversky VN, Kuznetsova IM, Turoverov KK, Zaslavsky B. Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates. FEBS Lett 2014;589:15-22. [PMID: 25436423 DOI: 10.1016/j.febslet.2014.11.028] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/10/2014] [Accepted: 11/19/2014] [Indexed: 12/25/2022]
374
Drobnak I, Braselmann E, Chaney JL, Leyton DL, Bernstein HD, Lithgow T, Luirink J, Nataro JP, Clark PL. Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion. Mol Microbiol 2014;95:1-16. [PMID: 25345653 DOI: 10.1111/mmi.12838] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2014] [Indexed: 01/02/2023]
375
Eickholt J, Wang Z. PCP-ML: protein characterization package for machine learning. BMC Res Notes 2014;7:810. [PMID: 25406415 PMCID: PMC4246511 DOI: 10.1186/1756-0500-7-810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 10/31/2014] [Indexed: 11/10/2022]  Open
376
Barman RK, Saha S, Das S. Prediction of interactions between viral and host proteins using supervised machine learning methods. PLoS One 2014;9:e112034. [PMID: 25375323 PMCID: PMC4223108 DOI: 10.1371/journal.pone.0112034] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 10/11/2014] [Indexed: 12/15/2022]  Open
377
Potenza E, Di Domenico T, Walsh I, Tosatto SCE. MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins. Nucleic Acids Res 2014;43:D315-20. [PMID: 25361972 PMCID: PMC4384034 DOI: 10.1093/nar/gku982] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
378
Structural protein reorganization and fold emergence investigated through amino acid sequence permutations. Amino Acids 2014;47:147-52. [PMID: 25331423 DOI: 10.1007/s00726-014-1849-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
379
Walsh I, Giollo M, Di Domenico T, Ferrari C, Zimmermann O, Tosatto SCE. Comprehensive large-scale assessment of intrinsic protein disorder. ACTA ACUST UNITED AC 2014;31:201-8. [PMID: 25246432 DOI: 10.1093/bioinformatics/btu625] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
380
Improved prediction of residue flexibility by embedding optimized amino acid grouping into RSA-based linear models. Amino Acids 2014;46:2665-80. [DOI: 10.1007/s00726-014-1817-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/21/2014] [Indexed: 11/26/2022]
381
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. From protein sequence to dynamics and disorder with DynaMine. Nat Commun 2014;4:2741. [PMID: 24225580 DOI: 10.1038/ncomms3741] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/10/2013] [Indexed: 11/09/2022]  Open
382
Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life. CELLULAR AND MOLECULAR LIFE SCIENCES : CMLS 2014. [PMID: 24939692 DOI: 10.1007/s00018‐014‐1661‐9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
383
Walsh I, Seno F, Tosatto SCE, Trovato A. PASTA 2.0: an improved server for protein aggregation prediction. Nucleic Acids Res 2014;42:W301-7. [PMID: 24848016 PMCID: PMC4086119 DOI: 10.1093/nar/gku399] [Citation(s) in RCA: 346] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
384
Giollo M, Martin AJM, Walsh I, Ferrari C, Tosatto SCE. NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation. BMC Genomics 2014;15 Suppl 4:S7. [PMID: 25057121 PMCID: PMC4083412 DOI: 10.1186/1471-2164-15-s4-s7] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
385
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acids Res 2014;42:W264-70. [PMID: 24728994 PMCID: PMC4086073 DOI: 10.1093/nar/gku270] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
386
Walsh I, Di Domenico T, Tosatto SCE. RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance. Amino Acids 2013;46:853-62. [PMID: 24363213 DOI: 10.1007/s00726-013-1645-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 12/11/2013] [Indexed: 11/25/2022]
387
Mao W, Cong P, Wang Z, Lu L, Zhu Z, Li T. NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data. PLoS One 2013;8:e83532. [PMID: 24376713 PMCID: PMC3871590 DOI: 10.1371/journal.pone.0083532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 11/04/2013] [Indexed: 11/28/2022]  Open
388
Becker J, Maes F, Wehenkel L. On the encoding of proteins for disordered regions prediction. PLoS One 2013;8:e82252. [PMID: 24358161 PMCID: PMC3864923 DOI: 10.1371/journal.pone.0082252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/21/2013] [Indexed: 12/02/2022]  Open
389
Mahani A, Henriksson J, Wright APH. Origins of Myc proteins--using intrinsic protein disorder to trace distant relatives. PLoS One 2013;8:e75057. [PMID: 24086436 PMCID: PMC3782479 DOI: 10.1371/journal.pone.0075057] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 08/09/2013] [Indexed: 01/10/2023]  Open
390
Peng Z, Mizianty MJ, Kurgan L. Genome-scale prediction of proteins with long intrinsically disordered regions. Proteins 2013;82:145-58. [PMID: 23798504 DOI: 10.1002/prot.24348] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/06/2013] [Indexed: 12/24/2022]
391
Jin F, Liu Z. Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins. Biophys J 2013;104:488-95. [PMID: 23442871 DOI: 10.1016/j.bpj.2012.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 11/17/2022]  Open
392
Wei Q, Dunbrack RL. The role of balanced training and testing data sets for binary classifiers in bioinformatics. PLoS One 2013;8:e67863. [PMID: 23874456 PMCID: PMC3706434 DOI: 10.1371/journal.pone.0067863] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 05/23/2013] [Indexed: 12/03/2022]  Open
393
Yan J, Mizianty MJ, Filipow PL, Uversky VN, Kurgan L. RAPID: fast and accurate sequence-based prediction of intrinsic disorder content on proteomic scale. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013;1834:1671-80. [PMID: 23732563 DOI: 10.1016/j.bbapap.2013.05.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/22/2013] [Indexed: 11/24/2022]
394
Di Domenico T, Walsh I, Tosatto SCE. Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. BMC Bioinformatics 2013;14 Suppl 7:S3. [PMID: 23815411 PMCID: PMC3633070 DOI: 10.1186/1471-2105-14-s7-s3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
395
DEIANA ANTONIO, GIANSANTI ANDREA. TUNING THE PRECISION OF PREDICTORS TO REDUCE OVERESTIMATION OF PROTEIN DISORDER OVER LARGE DATASETS. J Bioinform Comput Biol 2013;11:1250023. [DOI: 10.1142/s0219720012500230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
396
Xue B, Uversky VN. Structural characterizations of phosphorylatable residues in transmembrane proteins from Arabidopsis thaliana. INTRINSICALLY DISORDERED PROTEINS 2013;1:e25713. [PMID: 28516016 PMCID: PMC5424800 DOI: 10.4161/idp.25713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/28/2013] [Accepted: 07/10/2013] [Indexed: 12/26/2022]
397
Mizianty MJ, Peng Z, Kurgan L. MFDp2: Accurate predictor of disorder in proteins by fusion of disorder probabilities, content and profiles. INTRINSICALLY DISORDERED PROTEINS 2013;1:e24428. [PMID: 28516009 PMCID: PMC5424793 DOI: 10.4161/idp.24428] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 03/23/2013] [Indexed: 11/28/2022]
398
Fan X, Kurgan L. Accurate prediction of disorder in protein chains with a comprehensive and empirically designed consensus. J Biomol Struct Dyn 2013;32:448-64. [DOI: 10.1080/07391102.2013.775969] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Eickholt J, Cheng J. DNdisorder: predicting protein disorder using boosting and deep networks. BMC Bioinformatics 2013;14:88. [PMID: 23497251 PMCID: PMC3599628 DOI: 10.1186/1471-2105-14-88] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 02/28/2013] [Indexed: 11/23/2022]  Open
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HOWELL MARK, GREEN RYAN, KILLEEN ALEXIS, WEDDERBURN LAMAR, PICASCIO VINCENT, RABIONET ALEJANDRO, PENG ZHENLING, LARINA MAYA, XUE BIN, KURGAN LUKASZ, UVERSKY VLADIMIRN. NOT THAT RIGID MIDGETS AND NOT SO FLEXIBLE GIANTS: ON THE ABUNDANCE AND ROLES OF INTRINSIC DISORDER IN SHORT AND LONG PROTEINS. J BIOL SYST 2013. [DOI: 10.1142/s0218339012400086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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