IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding
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Wright, 1999, Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm, J. Mol. Biol., 293, 321, 10.1006/jmbi.1999.3110
van der Lee, 2014, Classification of intrinsically disordered regions and proteins, Chem. Rev., 114, 6589, 10.1021/cr400525m
Mészáros, 2007, Molecular principles of the interactions of disordered proteins, J. Mol. Biol., 372, 549, 10.1016/j.jmb.2007.07.004
Vacic, 2007, Characterization of molecular recognition features, MoRFs, and their binding partners, J. Proteome Res., 6, 2351, 10.1021/pr0701411
Van Roey, 2012, Motif switches: decision-making in cell regulation, Curr. Opin. Struct. Biol., 22, 378, 10.1016/j.sbi.2012.03.004
Borgia, 2018, Extreme disorder in an ultrahigh-affinity protein complex, Nature, 555, 61, 10.1038/nature25762
Miskei, 2017, FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies, Nucleic Acids Res., 45, D228, 10.1093/nar/gkw1019
Jakob, 2014, Conditionally and transiently disordered proteins: awakening cryptic disorder to regulate protein function, Chem. Rev., 114, 6779, 10.1021/cr400459c
Reichmann, 2012, Order out of disorder: working cycle of an intrinsically unfolded chaperone, Cell, 148, 947, 10.1016/j.cell.2012.01.045
Piovesan, 2017, DisProt 7.0: a major update of the database of disordered proteins, Nucleic Acids Res., 45, D219, 10.1093/nar/gkw1056
Ward, 2004, Prediction and functional analysis of native disorder in proteins from the three kingdoms of life, J. Mol. Biol., 337, 635, 10.1016/j.jmb.2004.02.002
Lobanov, 2015, How common is disorder? Occurrence of disordered residues in four domains of life, Int. J. Mol. Sci., 16, 19490, 10.3390/ijms160819490
Peng, 2015, Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life, Cell. Mol. Life Sci., 72, 137, 10.1007/s00018-014-1661-9
Xue, 2012, Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life, J. Biomol. Struct. Dyn., 30, 137, 10.1080/07391102.2012.675145
He, 2009, Predicting intrinsic disorder in proteins: an overview, Cell Res., 19, 929, 10.1038/cr.2009.87
Dosztányi, 2010, Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins, Brief. Bioinform., 11, 225, 10.1093/bib/bbp061
Meng, 2017, Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions, Cell. Mol. Life Sci., 74, 3069, 10.1007/s00018-017-2555-4
Dosztányi, 2005, The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins, J. Mol. Biol., 347, 827, 10.1016/j.jmb.2005.01.071
Dosztányi, 2005, IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content, Bioinformatics, 21, 3433, 10.1093/bioinformatics/bti541
Dosztányi, 2005, The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins, J. Mol. Biol., 347, 827, 10.1016/j.jmb.2005.01.071
Peng, 2012, Comprehensive comparative assessment of in-silico predictors of disordered regions, Curr. Protein Pept. Sci., 13, 6, 10.2174/138920312799277938
Walsh, 2015, Comprehensive large-scale assessment of intrinsic protein disorder, Bioinformatics, 31, 201, 10.1093/bioinformatics/btu625
Necci, 2018, A comprehensive assessment of long intrinsic protein disorder from the DisProt database, Bioinformatics, 34, 445, 10.1093/bioinformatics/btx590
Dosztányi, 2018, Prediction of protein disorder based on IUPred, Protein Sci., 27, 331, 10.1002/pro.3334
Peng, 2017, Prediction of disordered RNA, DNA, and protein binding regions using DisoRDPbind, Methods Mol. Biol., 1484, 187, 10.1007/978-1-4939-6406-2_14
Meng, 2016, DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences, Bioinformatics, 32, i341, 10.1093/bioinformatics/btw280
Mészáros, 2009, Prediction of protein binding regions in disordered proteins, PLoS Comput. Biol., 5, e1000376, 10.1371/journal.pcbi.1000376
Dosztányi, 2009, ANCHOR: web server for predicting protein binding regions in disordered proteins, Bioinformatics, 25, 2745, 10.1093/bioinformatics/btp518
Disfani, 2012, MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins, Bioinformatics, 28, i75, 10.1093/bioinformatics/bts209
Yan, 2016, Molecular recognition features (MoRFs) in three domains of life, Mol. Biosyst., 12, 697, 10.1039/C5MB00640F
Fang, 2013, MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation, BMC Bioinformatics, 14, 300, 10.1186/1471-2105-14-300
Jones, 2015, DISOPRED3: precise disordered region predictions with annotated protein-binding activity, Bioinformatics, 31, 857, 10.1093/bioinformatics/btu744
Malhis, 2015, Computational identification of MoRFs in protein sequences, Bioinformatics, 31, 1738, 10.1093/bioinformatics/btv060
Gibson, 2009, Cell regulation: determined to signal discrete cooperation, Trends Biochem. Sci., 34, 471, 10.1016/j.tibs.2009.06.007
Schad, 2018, DIBS: a repository of disordered binding sites mediating interactions with ordered proteins, Bioinformatics, 34, 535, 10.1093/bioinformatics/btx640
Reichmann, 2013, The roles of conditional disorder in redox proteins, Curr. Opin. Struct. Biol., 23, 436, 10.1016/j.sbi.2013.02.006
Fraga, 2017, Disulfide driven folding for a conditionally disordered protein, Sci. Rep., 7, 16994, 10.1038/s41598-017-17259-4
Gontero, 2012, An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle, Biochem. Soc. Trans., 40, 995, 10.1042/BST20120097
Thomas, 1996, An iterative method for extracting energy-like quantities from protein structures, Proc. Natl. Acad. Sci. U.S.A., 93, 11628, 10.1073/pnas.93.21.11628
Necci, 2017, MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins, Bioinformatics, 33, 1402, 10.1093/bioinformatics/btx015
Piovesan, 2018, MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins, Nucleic Acids Res., 46, D471, 10.1093/nar/gkx1071
Finn, 2017, InterPro in 2017-beyond protein family and domain annotations, Nucleic Acids Res., 45, D190, 10.1093/nar/gkw1107
Erdős, 2017, Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway, PLoS Comput. Biol., 13, e1005885, 10.1371/journal.pcbi.1005885
Reichmann, 2012, Order out of disorder: working cycle of an intrinsically unfolded chaperone, Cell, 148, 947, 10.1016/j.cell.2012.01.045
Pace, 2014, Zinc-binding cysteines: diverse functions and structural motifs, Biomolecules, 4, 419, 10.3390/biom4020419
Finn, 2016, The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res., 44, D279, 10.1093/nar/gkv1344
Hornbeck, 2015, PhosphoSitePlus, 2014: mutations, PTMs and recalibrations, Nucleic Acids Res., 43, D512, 10.1093/nar/gku1267
Fichó, 2017, MFIB: a repository of protein complexes with mutual folding induced by binding, Bioinformatics, 33, 3682, 10.1093/bioinformatics/btx486
Ferreon, 2013, Modulation of allostery by protein intrinsic disorder, Nature, 498, 390, 10.1038/nature12294
Egan, 1989, Binding of the Rb1 protein to E1A products is required for adenovirus transformation, Oncogene, 4, 383
Lowe, 1993, Stabilization of the p53 tumor suppressor is induced by adenovirus 5 E1A and accompanies apoptosis, Genes Dev., 7, 535, 10.1101/gad.7.4.535
Tremblay, 1988, Identification of the phosphorylation sites in early region 1A proteins of adenovirus type 5 by amino acid sequencing of peptide fragments, J. Biol. Chem., 263, 6375, 10.1016/S0021-9258(18)68796-4
Zou, 2002, Oxidation of the zinc-thiolate complex and uncoupling of endothelial nitric oxide synthase by peroxynitrite, J. Clin. Invest., 109, 817, 10.1172/JCI0214442