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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]

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Number Cited by Other Article(s)
151
Kagami LP, Orlando G, Raimondi D, Ancien F, Dixit B, Gavaldá-García J, Ramasamy P, Roca-Martínez J, Tzavella K, Vranken W. b2bTools: online predictions for protein biophysical features and their conservation. Nucleic Acids Res 2021;49:W52-W59. [PMID: 34057475 PMCID: PMC8262692 DOI: 10.1093/nar/gkab425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/21/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022]  Open
152
Oldfield CJ, Peng Z, Kurgan L. Disordered RNA-Binding Region Prediction with DisoRDPbind. Methods Mol Biol 2021;2106:225-239. [PMID: 31889261 DOI: 10.1007/978-1-0716-0231-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
153
Emenecker RJ, Holehouse AS, Strader LC. Biological Phase Separation and Biomolecular Condensates in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021;72:17-46. [PMID: 33684296 PMCID: PMC8221409 DOI: 10.1146/annurev-arplant-081720-015238] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
154
Association between Predicted Effects of TP53 Missense Variants on Protein Conformation and Their Phenotypic Presentation as Li-Fraumeni Syndrome or Hereditary Breast Cancer. Int J Mol Sci 2021;22:ijms22126345. [PMID: 34198491 PMCID: PMC8231809 DOI: 10.3390/ijms22126345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/18/2022]  Open
155
Verbiest MA, Delucchi M, Bilgin Sonay T, Anisimova M. Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer. FRONTIERS IN BIOINFORMATICS 2021;1:685844. [DOI: 10.3389/fbinf.2021.685844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/21/2021] [Indexed: 12/28/2022]  Open
156
Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins. J Proteome Res 2021;20:2704-2713. [PMID: 33719450 DOI: 10.1021/acs.jproteome.1c00011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
157
Vidal RL, Sepulveda D, Troncoso-Escudero P, Garcia-Huerta P, Gonzalez C, Plate L, Jerez C, Canovas J, Rivera CA, Castillo V, Cisternas M, Leal S, Martinez A, Grandjean J, Sonia D, Lashuel HA, Martin AJM, Latapiat V, Matus S, Sardi SP, Wiseman RL, Hetz C. Enforced dimerization between XBP1s and ATF6f enhances the protective effects of the UPR in models of neurodegeneration. Mol Ther 2021;29:1862-1882. [PMID: 33545358 PMCID: PMC8116614 DOI: 10.1016/j.ymthe.2021.01.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/14/2020] [Accepted: 01/21/2021] [Indexed: 02/07/2023]  Open
158
Katuwawala A, Ghadermarzi S, Hu G, Wu Z, Kurgan L. QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores. Comput Struct Biotechnol J 2021;19:2597-2606. [PMID: 34025946 PMCID: PMC8122155 DOI: 10.1016/j.csbj.2021.04.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 12/13/2022]  Open
159
Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. Brief Bioinform 2021;22:6231751. [PMID: 33866372 DOI: 10.1093/bib/bbab145] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/17/2021] [Accepted: 03/26/2021] [Indexed: 12/22/2022]  Open
160
Identification of Intrinsically Disordered Protein Regions Based on Deep Neural Network-VGG16. ALGORITHMS 2021. [DOI: 10.3390/a14040107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
161
MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation. Commun Biol 2021;4:414. [PMID: 33772081 PMCID: PMC7997880 DOI: 10.1038/s42003-021-01930-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023]  Open
162
Brandi V, Polticelli F. In Silico Analysis of Huntingtin Homologs in Lower Eukaryotes. Int J Mol Sci 2021;22:3214. [PMID: 33809947 PMCID: PMC8004120 DOI: 10.3390/ijms22063214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022]  Open
163
Zhao B, Katuwawala A, Uversky VN, Kurgan L. IDPology of the living cell: intrinsic disorder in the subcellular compartments of the human cell. Cell Mol Life Sci 2021;78:2371-2385. [PMID: 32997198 PMCID: PMC11071772 DOI: 10.1007/s00018-020-03654-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/09/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022]
164
Monzon AM, Bonato P, Necci M, Tosatto SCE, Piovesan D. FLIPPER: Predicting and Characterizing Linear Interacting Peptides in the Protein Data Bank. J Mol Biol 2021;433:166900. [PMID: 33647288 DOI: 10.1016/j.jmb.2021.166900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/31/2022]
165
Scheer H, de Almeida C, Ferrier E, Simonnot Q, Poirier L, Pflieger D, Sement FM, Koechler S, Piermaria C, Krawczyk P, Mroczek S, Chicher J, Kuhn L, Dziembowski A, Hammann P, Zuber H, Gagliardi D. The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. Nat Commun 2021;12:1298. [PMID: 33637717 PMCID: PMC7910438 DOI: 10.1038/s41467-021-21382-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/19/2021] [Indexed: 12/15/2022]  Open
166
Shen B, Chen Z, Yu C, Chen T, Shi M, Li T. Computational Screening of Phase-separating Proteins. GENOMICS PROTEOMICS & BIOINFORMATICS 2021;19:13-24. [PMID: 33610793 PMCID: PMC8498823 DOI: 10.1016/j.gpb.2020.11.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 11/17/2020] [Accepted: 12/10/2020] [Indexed: 11/27/2022]
167
Alshehri MA, Manee MM, Alqahtani FH, Al-Shomrani BM, Uversky VN. On the Prevalence and Potential Functionality of an Intrinsic Disorder in the MERS-CoV Proteome. Viruses 2021;13:v13020339. [PMID: 33671602 PMCID: PMC7926987 DOI: 10.3390/v13020339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/14/2022]  Open
168
Preto J, Krimm I. The intrinsically disordered N-terminus of the voltage-dependent anion channel. PLoS Comput Biol 2021;17:e1008750. [PMID: 33577583 PMCID: PMC7906469 DOI: 10.1371/journal.pcbi.1008750] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/25/2021] [Accepted: 01/27/2021] [Indexed: 01/08/2023]  Open
169
Gao C, Ma C, Wang H, Zhong H, Zang J, Zhong R, He F, Yang D. Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions. Sci Rep 2021;11:2985. [PMID: 33542394 PMCID: PMC7862400 DOI: 10.1038/s41598-021-82656-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/22/2021] [Indexed: 11/09/2022]  Open
170
Harnessing Machine Learning To Unravel Protein Degradation in Escherichia coli. mSystems 2021;6:6/1/e01296-20. [PMID: 33531410 PMCID: PMC7857536 DOI: 10.1128/msystems.01296-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
171
Using a low correlation high orthogonality feature set and machine learning methods to identify plant pentatricopeptide repeat coding gene/protein. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2020.02.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
172
Almog G, Olabode AS, Poon AFY. Tuning intrinsic disorder predictors for virus proteins. Virus Evol 2021;7:veaa106. [PMID: 33614158 PMCID: PMC7882063 DOI: 10.1093/ve/veaa106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
173
Kozono T, Sato H, Okumura W, Jogano C, Tamura-Nakano M, Kawamura YI, Rohrer J, Tonozuka T, Nishikawa A. The N-terminal region of Jaw1 has a role to inhibit the formation of organized smooth endoplasmic reticulum as an intrinsically disordered region. Sci Rep 2021;11:753. [PMID: 33436890 PMCID: PMC7804115 DOI: 10.1038/s41598-020-80258-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]  Open
174
Hon J, Marusiak M, Martinek T, Kunka A, Zendulka J, Bednar D, Damborsky J. SoluProt: Prediction of Soluble Protein Expression in Escherichia coli. Bioinformatics 2021;37:23-28. [PMID: 33416864 PMCID: PMC8034534 DOI: 10.1093/bioinformatics/btaa1102] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/05/2020] [Accepted: 12/28/2020] [Indexed: 12/17/2022]  Open
175
Piovesan D, Necci M, Escobedo N, Monzon AM, Hatos A, Mičetić I, Quaglia F, Paladin L, Ramasamy P, Dosztányi Z, Vranken WF, Davey N, Parisi G, Fuxreiter M, Tosatto SE. MobiDB: intrinsically disordered proteins in 2021. Nucleic Acids Res 2021;49:D361-D367. [PMID: 33237329 PMCID: PMC7779018 DOI: 10.1093/nar/gkaa1058] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/16/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022]  Open
176
Kurgan L, Li M, Li Y. The Methods and Tools for Intrinsic Disorder Prediction and their Application to Systems Medicine. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11320-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]  Open
177
Critical assessment of protein intrinsic disorder prediction. Nat Methods 2021;18:472-481. [PMID: 33875885 PMCID: PMC8105172 DOI: 10.1038/s41592-021-01117-3] [Citation(s) in RCA: 202] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023]
178
Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Cerqueda-García D, Castaño E, Rodríguez-Zapata LC. Towards an understanding of the role of intrinsic protein disorder on plant adaptation to environmental challenges. Cell Stress Chaperones 2021;26:141-150. [PMID: 32902806 PMCID: PMC7736417 DOI: 10.1007/s12192-020-01162-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/31/2020] [Accepted: 08/27/2020] [Indexed: 02/05/2023]  Open
179
Hardenberg M, Horvath A, Ambrus V, Fuxreiter M, Vendruscolo M. Widespread occurrence of the droplet state of proteins in the human proteome. Proc Natl Acad Sci U S A 2020;117:33254-33262. [PMID: 33318217 PMCID: PMC7777240 DOI: 10.1073/pnas.2007670117] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
180
Zhu Z, Chen H, Liu L, Cao Y, Jiang T, Zou Y, Peng Y. Classification and characterization of multigene family proteins of African swine fever viruses. Brief Bioinform 2020;22:6041169. [PMID: 33333556 DOI: 10.1093/bib/bbaa380] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/14/2020] [Accepted: 11/27/2020] [Indexed: 12/25/2022]  Open
181
Necci M, Piovesan D, Clementel D, Dosztányi Z, Tosatto SCE. MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavours in proteins. Bioinformatics 2020;36:5533-5534. [PMID: 33325498 DOI: 10.1093/bioinformatics/btaa1045] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/03/2020] [Accepted: 12/07/2020] [Indexed: 12/31/2022]  Open
182
Palopoli N, Marchetti J, Monzon AM, Zea DJ, Tosatto SCE, Fornasari MS, Parisi G. Intrinsically Disordered Protein Ensembles Shape Evolutionary Rates Revealing Conformational Patterns. J Mol Biol 2020;433:166751. [PMID: 33310020 DOI: 10.1016/j.jmb.2020.166751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022]
183
Katuwawala A, Kurgan L. Comparative Assessment of Intrinsic Disorder Predictions with a Focus on Protein and Nucleic Acid-Binding Proteins. Biomolecules 2020;10:E1636. [PMID: 33291838 PMCID: PMC7762010 DOI: 10.3390/biom10121636] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/26/2020] [Accepted: 12/03/2020] [Indexed: 01/18/2023]  Open
184
The exquisite structural biophysics of the Golgi Reassembly and Stacking Proteins. Int J Biol Macromol 2020;164:3632-3644. [DOI: 10.1016/j.ijbiomac.2020.08.203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022]
185
Cusick JK, Alhomsy Y, Wong S, Talbott G, Uversky VN, Hart C, Hejazi N, Jacobs AT, Shi Y. RELT stains prominently in B-cell lymphomas and binds the hematopoietic transcription factor MDFIC. Biochem Biophys Rep 2020;24:100868. [PMID: 33367115 PMCID: PMC7749370 DOI: 10.1016/j.bbrep.2020.100868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/02/2020] [Accepted: 11/23/2020] [Indexed: 11/30/2022]  Open
186
Antonić DD, Subotić AR, Dragićević MB, Pantelić D, Milošević SM, Simonović AD, Momčilović I. Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana. PLANTS (BASEL, SWITZERLAND) 2020;9:E1589. [PMID: 33212846 PMCID: PMC7698297 DOI: 10.3390/plants9111589] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
187
Hesgrove C, Boothby TC. The biology of tardigrade disordered proteins in extreme stress tolerance. Cell Commun Signal 2020;18:178. [PMID: 33148259 PMCID: PMC7640644 DOI: 10.1186/s12964-020-00670-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]  Open

Video Abstract

  • Cherie Hesgrove
    • Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
  • Thomas C Boothby
    • Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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188
Zhu L, Cheng H, Peng G, Wang S, Zhang Z, Ni E, Fu X, Zhuang C, Liu Z, Zhou H. Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles. GENOMICS PROTEOMICS & BIOINFORMATICS 2020;18:305-320. [PMID: 33147495 PMCID: PMC7801245 DOI: 10.1016/j.gpb.2019.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 12/06/2018] [Accepted: 01/11/2019] [Indexed: 02/04/2023]
189
Ambrus V, Hoffka G, Fuxreiter M. Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer. Sci Rep 2020;10:18866. [PMID: 33139795 PMCID: PMC7608688 DOI: 10.1038/s41598-020-75772-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/16/2020] [Indexed: 11/09/2022]  Open
190
Malhis N, Jacobson M, Jones SJM, Gsponer J. LIST-S2: taxonomy based sorting of deleterious missense mutations across species. Nucleic Acids Res 2020;48:W154-W161. [PMID: 32352516 PMCID: PMC7319545 DOI: 10.1093/nar/gkaa288] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/05/2020] [Accepted: 04/19/2020] [Indexed: 12/18/2022]  Open
191
McClatchy DB, Martínez-Bartolomé S, Gao Y, Lavallée-Adam M, Yates JR. Quantitative analysis of global protein stability rates in tissues. Sci Rep 2020;10:15983. [PMID: 32994440 PMCID: PMC7524747 DOI: 10.1038/s41598-020-72410-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]  Open
192
Van Bibber NW, Haerle C, Khalife R, Dayhoff GW, Uversky VN. Intrinsic Disorder in Human Proteins Encoded by Core Duplicon Gene Families. J Phys Chem B 2020;124:8050-8070. [PMID: 32880174 DOI: 10.1021/acs.jpcb.0c07676] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
193
Li Q, Wang X, Dou Z, Yang W, Huang B, Lou J, Zhang Z. Protein Databases Related to Liquid-Liquid Phase Separation. Int J Mol Sci 2020;21:E6796. [PMID: 32947964 PMCID: PMC7555049 DOI: 10.3390/ijms21186796] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 01/16/2023]  Open
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Livingstone I, Uversky VN, Furniss D, Wiberg A. The Pathophysiological Significance of Fibulin-3. Biomolecules 2020;10:E1294. [PMID: 32911658 PMCID: PMC7563619 DOI: 10.3390/biom10091294] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]  Open
195
Yu C, Shen B, You K, Huang Q, Shi M, Wu C, Chen Y, Zhang C, Li T. Proteome-scale analysis of phase-separated proteins in immunofluorescence images. Brief Bioinform 2020;22:5900570. [PMID: 34020549 DOI: 10.1093/bib/bbaa187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/25/2022]  Open
196
Weisz J, Uversky VN. Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners. Int J Mol Sci 2020;21:ijms21165879. [PMID: 32824294 PMCID: PMC7461550 DOI: 10.3390/ijms21165879] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]  Open
197
Nemoto M, Iwaki S, Moriya H, Monden Y, Tamura T, Inagaki K, Mayama S, Obuse K. Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020;22:551-563. [PMID: 32488507 DOI: 10.1007/s10126-020-09976-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
198
Ai G, Yang K, Ye W, Tian Y, Du Y, Zhu H, Li T, Xia Q, Shen D, Peng H, Jing M, Xia A, Dou D. Prediction and Characterization of RXLR Effectors in Pythium Species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020;33:1046-1058. [PMID: 32330072 DOI: 10.1094/mpmi-01-20-0010-r] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
199
Exploring Protein Intrinsic Disorder with MobiDB. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020;2141:127-143. [PMID: 32696355 DOI: 10.1007/978-1-0716-0524-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
200
Monzon AM, Necci M, Quaglia F, Walsh I, Zanotti G, Piovesan D, Tosatto SCE. Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. Int J Mol Sci 2020;21:ijms21124496. [PMID: 32599863 PMCID: PMC7349999 DOI: 10.3390/ijms21124496] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/12/2023]  Open
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