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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)
51
Yan K, Ji Q, Zhao D, Li M, Sun X, Wang Z, Liu X, Liu Z, Li H, Ding Y, Wang S, Belmonte JCI, Qu J, Zhang W, Liu GH. SGF29 nuclear condensates reinforce cellular aging. Cell Discov 2023;9:110. [PMID: 37935676 PMCID: PMC10630320 DOI: 10.1038/s41421-023-00602-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/07/2023] [Indexed: 11/09/2023]  Open
52
Basu S, Hegedűs T, Kurgan L. CoMemMoRFPred: Sequence-based Prediction of MemMoRFs by Combining Predictors of Intrinsic Disorder, MoRFs and Disordered Lipid-binding Regions. J Mol Biol 2023;435:168272. [PMID: 37709009 DOI: 10.1016/j.jmb.2023.168272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
53
Kurgan L, Hu G, Wang K, Ghadermarzi S, Zhao B, Malhis N, Erdős G, Gsponer J, Uversky VN, Dosztányi Z. Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins. Nat Protoc 2023;18:3157-3172. [PMID: 37740110 DOI: 10.1038/s41596-023-00876-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/21/2023] [Indexed: 09/24/2023]
54
Ohki Y, Shinone T, Inoko S, Sudo M, Demura M, Kikukawa T, Tsukamoto T. The preferential transport of NO3- by full-length Guillardia theta anion channelrhodopsin 1 is enhanced by its extended cytoplasmic domain. J Biol Chem 2023;299:105305. [PMID: 37778732 PMCID: PMC10637977 DOI: 10.1016/j.jbc.2023.105305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]  Open
55
Djulbegovic M, Taylor Gonzalez DJ, Antonietti M, Uversky VN, Shields CL, Karp CL. Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma. Int J Biol Macromol 2023;250:126027. [PMID: 37506796 PMCID: PMC11182630 DOI: 10.1016/j.ijbiomac.2023.126027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
56
Németh-Szatmári O, Nagy-Mikó B, Györkei Á, Varga D, Kovács BBH, Igaz N, Bognár B, Rázga Z, Nagy G, Zsindely N, Bodai L, Papp B, Erdélyi M, Kiricsi M, Blastyák A, Collart MA, Boros IM, Villányi Z. Phase-separated ribosome-nascent chain complexes in genotoxic stress response. RNA (NEW YORK, N.Y.) 2023;29:1557-1574. [PMID: 37460154 PMCID: PMC10578487 DOI: 10.1261/rna.079755.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 09/20/2023]
57
Wang Y, Yu C, Pei G, Jia W, Li T, Li P. Dissolution of oncofusion transcription factor condensates for cancer therapy. Nat Chem Biol 2023;19:1223-1234. [PMID: 37400539 DOI: 10.1038/s41589-023-01376-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
58
Zhou S, Zhou Y, Liu T, Zheng J, Jia C. PredLLPS_PSSM: a novel predictor for liquid-liquid protein separation identification based on evolutionary information and a deep neural network. Brief Bioinform 2023;24:bbad299. [PMID: 37609923 DOI: 10.1093/bib/bbad299] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023]  Open
59
Tang YJ, Yan K, Zhang X, Tian Y, Liu B. Protein intrinsically disordered region prediction by combining neural architecture search and multi-objective genetic algorithm. BMC Biol 2023;21:188. [PMID: 37674132 PMCID: PMC10483879 DOI: 10.1186/s12915-023-01672-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023]  Open
60
Denesyuk AI, Permyakov SE, Permyakov EA, Johnson MS, Denessiouk K, Uversky VN. Canonical structural-binding modes in the calmodulin-target protein complexes. J Biomol Struct Dyn 2023;41:7582-7594. [PMID: 36106955 DOI: 10.1080/07391102.2022.2123391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
61
Derbyshire MC, Raffaele S. Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors. Nat Commun 2023;14:5244. [PMID: 37640704 PMCID: PMC10462633 DOI: 10.1038/s41467-023-40949-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]  Open
62
Zhu P, Hou C, Liu M, Chen T, Li T, Wang L. Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol. BMC Genomics 2023;24:493. [PMID: 37641002 PMCID: PMC10464338 DOI: 10.1186/s12864-023-09600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023]  Open
63
Antonietti M, Gonzalez DJT, Djulbegovic M, Dayhoff GW, Uversky VN, Shields CL, Karp CL. Intrinsic disorder in PRAME and its role in uveal melanoma. Cell Commun Signal 2023;21:222. [PMID: 37626310 PMCID: PMC10463658 DOI: 10.1186/s12964-023-01197-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/13/2023] [Indexed: 08/27/2023]  Open
64
Mokin YI, Gavrilova AA, Fefilova AS, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. Nucleolar- and Nuclear-Stress-Induced Membrane-Less Organelles: A Proteome Analysis through the Prism of Liquid-Liquid Phase Separation. Int J Mol Sci 2023;24:11007. [PMID: 37446185 DOI: 10.3390/ijms241311007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]  Open
65
Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023;9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023]  Open
66
Zhao B, Ghadermarzi S, Kurgan L. Comparative evaluation of AlphaFold2 and disorder predictors for prediction of intrinsic disorder, disorder content and fully disordered proteins. Comput Struct Biotechnol J 2023;21:3248-3258. [PMID: 38213902 PMCID: PMC10782001 DOI: 10.1016/j.csbj.2023.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 01/13/2024]  Open
67
Redl I, Fisicaro C, Dutton O, Hoffmann F, Henderson L, Owens BJ, Heberling M, Paci E, Tamiola K. ADOPT: intrinsic protein disorder prediction through deep bidirectional transformers. NAR Genom Bioinform 2023;5:lqad041. [PMID: 37138579 PMCID: PMC10150328 DOI: 10.1093/nargab/lqad041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/07/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]  Open
68
Uversky VN, Kurgan L. Overview Update: Computational Prediction of Intrinsic Disorder in Proteins. Curr Protoc 2023;3:e802. [PMID: 37310199 DOI: 10.1002/cpz1.802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
69
Reinar WB, Greulich A, Stø IM, Knutsen JB, Reitan T, Tørresen OK, Jentoft S, Butenko MA, Jakobsen KS. Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. SCIENCE ADVANCES 2023;9:eadd6960. [PMID: 36947624 PMCID: PMC10032594 DOI: 10.1126/sciadv.add6960] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
70
Jiang P, Cai R, Lugo-Martinez J, Guo Y. A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation. Brief Bioinform 2023;24:7031681. [PMID: 36754843 DOI: 10.1093/bib/bbad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/21/2022] [Accepted: 01/01/2023] [Indexed: 02/10/2023]  Open
71
Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis. Nat Commun 2023;14:1329. [PMID: 36898987 PMCID: PMC10006080 DOI: 10.1038/s41467-023-37017-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023]  Open
72
Mínguez-Toral M, Pacios LF, Sánchez F, Ponz F. Structural intrinsic disorder in a functionalized potyviral coat protein as a main viability determinant of its assembled nanoparticles. Int J Biol Macromol 2023;236:123958. [PMID: 36906197 DOI: 10.1016/j.ijbiomac.2023.123958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/24/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023]
73
Computational prediction of disordered binding regions. Comput Struct Biotechnol J 2023;21:1487-1497. [PMID: 36851914 PMCID: PMC9957716 DOI: 10.1016/j.csbj.2023.02.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]  Open
74
Roy A, Chan Mine E, Gaifas L, Leyrat C, Volchkova VA, Baudin F, Martinez-Gil L, Volchkov VE, Karlin DG, Bourhis JM, Jamin M. Orthoparamyxovirinae C Proteins Have a Common Origin and a Common Structural Organization. Biomolecules 2023;13:biom13030455. [PMID: 36979390 PMCID: PMC10046310 DOI: 10.3390/biom13030455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023]  Open
75
Kouros CE, Makri V, Ouzounis CA, Chasapi A. Disease association and comparative genomics of compositional bias in human proteins. F1000Res 2023;12:198. [PMID: 37082000 PMCID: PMC10111144 DOI: 10.12688/f1000research.129929.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2023] [Indexed: 02/22/2023]  Open
76
Kouros CE, Makri V, Ouzounis CA, Chasapi A. Disease association and comparative genomics of compositional bias in human proteins. F1000Res 2023;12:198. [PMID: 37082000 PMCID: PMC10111144 DOI: 10.12688/f1000research.129929.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2023] [Indexed: 04/25/2023]  Open
77
Han B, Ren C, Wang W, Li J, Gong X. Computational Prediction of Protein Intrinsically Disordered Region Related Interactions and Functions. Genes (Basel) 2023;14:432. [PMID: 36833360 PMCID: PMC9956190 DOI: 10.3390/genes14020432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]  Open
78
Liaisons dangereuses: Intrinsic Disorder in Cellular Proteins Recruited to Viral Infection-Related Biocondensates. Int J Mol Sci 2023;24:ijms24032151. [PMID: 36768473 PMCID: PMC9917183 DOI: 10.3390/ijms24032151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023]  Open
79
Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M. Evolution of the orthopoxvirus core genome. Virus Res 2023;323:198975. [PMID: 36280003 PMCID: PMC9586335 DOI: 10.1016/j.virusres.2022.198975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
80
Lahorkar A, Bhosale H, Sane A, Ramakrishnan V, Jayaraman VK. Identification of Phase Separating Proteins With Distributed Reduced Alphabet Representations of Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:410-420. [PMID: 35139023 DOI: 10.1109/tcbb.2022.3149310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
81
Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a. Int J Mol Sci 2022;23:ijms232315291. [PMID: 36499617 PMCID: PMC9738585 DOI: 10.3390/ijms232315291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]  Open
82
Martinez P, Patel H, You Y, Jury N, Perkins A, Lee-Gosselin A, Taylor X, You Y, Viana Di Prisco G, Huang X, Dutta S, Wijeratne AB, Redding-Ochoa J, Shahid SS, Codocedo JF, Min S, Landreth GE, Mosley AL, Wu YC, McKinzie DL, Rochet JC, Zhang J, Atwood BK, Troncoso J, Lasagna-Reeves CA. Bassoon contributes to tau-seed propagation and neurotoxicity. Nat Neurosci 2022;25:1597-1607. [PMID: 36344699 PMCID: PMC9708566 DOI: 10.1038/s41593-022-01191-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
83
Malaney P, Benitez O, Zhang X, Post SM. Assessing the role of intrinsic disorder in RNA-binding protein function: hnRNP K as a case study. Methods 2022;208:59-65. [DOI: 10.1016/j.ymeth.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/20/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022]  Open
84
Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity. Biomolecules 2022;12:biom12121771. [PMID: 36551199 PMCID: PMC9775558 DOI: 10.3390/biom12121771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]  Open
85
Piovesan D, Del Conte A, Clementel D, Monzon A, Bevilacqua M, Aspromonte M, Iserte J, Orti FE, Marino-Buslje C, Tosatto SE. MobiDB: 10 years of intrinsically disordered proteins. Nucleic Acids Res 2022;51:D438-D444. [PMID: 36416266 PMCID: PMC9825420 DOI: 10.1093/nar/gkac1065] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/11/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022]  Open
86
Horvath A, Vendruscolo M, Fuxreiter M. Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates. Biochemistry 2022;61:2461-2469. [DOI: 10.1021/acs.biochem.2c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
87
Fang M, He Y, Du Z, Uversky VN. DeepCLD: An Efficient Sequence-Based Predictor of Intrinsically Disordered Proteins. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3154-3159. [PMID: 34727037 DOI: 10.1109/tcbb.2021.3124273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
88
Ilzhöfer D, Heinzinger M, Rost B. SETH predicts nuances of residue disorder from protein embeddings. FRONTIERS IN BIOINFORMATICS 2022;2:1019597. [PMID: 36304335 PMCID: PMC9580958 DOI: 10.3389/fbinf.2022.1019597] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]  Open
89
Dhulipala S, Uversky VN. Looking at the Pathogenesis of the Rabies Lyssavirus Strain Pasteur Vaccins through a Prism of the Disorder-Based Bioinformatics. Biomolecules 2022;12:1436. [PMID: 36291645 PMCID: PMC9599798 DOI: 10.3390/biom12101436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022]  Open
90
Chen R, Li X, Yang Y, Song X, Wang C, Qiao D. Prediction of protein-protein interaction sites in intrinsically disordered proteins. Front Mol Biosci 2022;9:985022. [PMID: 36250006 PMCID: PMC9567019 DOI: 10.3389/fmolb.2022.985022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022]  Open
91
Djulbegovic MB, Taylor DJ, Uversky VN, Galor A, Shields CL, Karp CL. Intrinsic Disorder in BAP1 and Its Association with Uveal Melanoma. Genes (Basel) 2022;13:1703. [PMID: 36292588 PMCID: PMC9601668 DOI: 10.3390/genes13101703] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]  Open
92
Selvaraj C, Pravin MA, Alhoqail WA, Nayarisseri A, Singh SK. Intrinsically disordered proteins in viral pathogenesis and infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022;132:221-242. [PMID: 36088077 DOI: 10.1016/bs.apcsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
93
Ahmad A, Uversky VN, Khan RH. Aberrant liquid-liquid phase separation and amyloid aggregation of proteins related to neurodegenerative diseases. Int J Biol Macromol 2022;220:703-720. [PMID: 35998851 DOI: 10.1016/j.ijbiomac.2022.08.132] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/05/2022]
94
Roca-Martinez J, Lazar T, Gavalda-Garcia J, Bickel D, Pancsa R, Dixit B, Tzavella K, Ramasamy P, Sanchez-Fornaris M, Grau I, Vranken WF. Challenges in describing the conformation and dynamics of proteins with ambiguous behavior. Front Mol Biosci 2022;9:959956. [PMID: 35992270 PMCID: PMC9382080 DOI: 10.3389/fmolb.2022.959956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022]  Open
95
Ganne A, Balasubramaniam M, Ayyadevara S, Shmookler Reis RJ. Machine-learning analysis of intrinsically disordered proteins identifies key factors that contribute to neurodegeneration-related aggregation. Front Aging Neurosci 2022;14:938117. [PMID: 35992603 PMCID: PMC9382113 DOI: 10.3389/fnagi.2022.938117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022]  Open
96
Intrinsically disordered BMP4 morphogen and the beak of the finch: Co-option of an ancient axial patterning system. Int J Biol Macromol 2022;219:366-373. [PMID: 35931296 DOI: 10.1016/j.ijbiomac.2022.07.203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/25/2022] [Indexed: 12/24/2022]
97
Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022;11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
98
Mignon J, Mottet D, Leyder T, Uversky VN, Perpète EA, Michaux C. Structural characterisation of amyloidogenic intrinsically disordered zinc finger protein isoforms DPF3b and DPF3a. Int J Biol Macromol 2022;218:57-71. [PMID: 35863661 DOI: 10.1016/j.ijbiomac.2022.07.102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 11/05/2022]
99
Hou C, Li Y, Wang M, Wu H, Li T. Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning. BMC Biol 2022;20:162. [PMID: 35836176 PMCID: PMC9281121 DOI: 10.1186/s12915-022-01364-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/29/2022] [Indexed: 01/06/2023]  Open
100
Horvath A, Fuxreiter M, Vendruscolo M, Holt C, Carver JA. Are casein micelles extracellular condensates formed by liquid-liquid phase separation? FEBS Lett 2022;596:2072-2085. [PMID: 35815989 DOI: 10.1002/1873-3468.14449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022]
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