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For: Lobanov MY, Klus P, Sokolovsky IV, Tartaglia GG, Galzitskaya OV. Non-random distribution of homo-repeats: links with biological functions and human diseases. Sci Rep 2016;6:26941. [PMID: 27256590 DOI: 10.1038/srep26941] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/06/2016] [Indexed: 12/22/2022]  Open
Number Cited by Other Article(s)
1
Bonet DF, Ranyai S, Aswad L, Lane DP, Arsenian-Henriksson M, Landreh M, Lama D. AlphaFold with conformational sampling reveals the structural landscape of homorepeats. Structure 2024:S0969-2126(24)00333-2. [PMID: 39299235 DOI: 10.1016/j.str.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/27/2024] [Accepted: 08/23/2024] [Indexed: 09/22/2024]
2
Teekas L, Sharma S, Vijay N. Terminal regions of a protein are a hotspot for low complexity regions and selection. Open Biol 2024;14:230439. [PMID: 38862022 DOI: 10.1098/rsob.230439] [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: 12/01/2023] [Accepted: 05/13/2024] [Indexed: 06/13/2024]  Open
3
Elena-Real CA, Mier P, Sibille N, Andrade-Navarro MA, Bernadó P. Structure-function relationships in protein homorepeats. Curr Opin Struct Biol 2023;83:102726. [PMID: 37924569 DOI: 10.1016/j.sbi.2023.102726] [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: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
4
Barbosa Pereira PJ, Manso JA, Macedo-Ribeiro S. The structural plasticity of polyglutamine repeats. Curr Opin Struct Biol 2023;80:102607. [PMID: 37178477 DOI: 10.1016/j.sbi.2023.102607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/15/2023]
5
Ibtehaz N, Sourav SMSH, Bayzid MS, Rahman MS. Align-gram: Rethinking the Skip-gram Model for Protein Sequence Analysis. Protein J 2023;42:135-146. [PMID: 36977849 DOI: 10.1007/s10930-023-10096-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/29/2023]
6
Ito Y, Chadani Y, Niwa T, Yamakawa A, Machida K, Imataka H, Taguchi H. Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes. Nat Commun 2022;13:7451. [PMID: 36460666 PMCID: PMC9718836 DOI: 10.1038/s41467-022-35156-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022]  Open
7
Mier P, Elena-Real CA, Cortés J, Bernadó P, Andrade-Navarro MA. The sequence context in poly-alanine regions: structure, function and conservation. Bioinformatics 2022;38:4851-4858. [PMID: 36106994 PMCID: PMC9620824 DOI: 10.1093/bioinformatics/btac610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 07/07/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022]  Open
8
Cascarina SM, Ross ED. Expansion and functional analysis of the SR-related protein family across the domains of life. RNA (NEW YORK, N.Y.) 2022;28:1298-1314. [PMID: 35863866 PMCID: PMC9479744 DOI: 10.1261/rna.079170.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
9
Mier P, Andrade-Navarro MA. Regions with two amino acids in protein sequences: a step forward from homorepeats into the low complexity landscape. Comput Struct Biotechnol J 2022;20:5516-5523. [PMID: 36249567 PMCID: PMC9550522 DOI: 10.1016/j.csbj.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022]  Open
10
Chakrabarty B, Parekh N. DbStRiPs: Database of structural repeats in proteins. Protein Sci 2022;31:23-36. [PMID: 33641184 PMCID: PMC8740836 DOI: 10.1002/pro.4052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 01/03/2023]
11
Eaton AF, Brown D, Merkulova M. The evolutionary conserved TLDc domain defines a new class of (H+)V-ATPase interacting proteins. Sci Rep 2021;11:22654. [PMID: 34811399 PMCID: PMC8608904 DOI: 10.1038/s41598-021-01809-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/02/2021] [Indexed: 01/26/2023]  Open
12
Mier P, Andrade-Navarro MA. Between Interactions and Aggregates: The PolyQ Balance. Genome Biol Evol 2021;13:evab246. [PMID: 34791220 PMCID: PMC8763233 DOI: 10.1093/gbe/evab246] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 11/17/2022]  Open
13
Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
14
Cascarina SM, King DC, Osborne Nishimura E, Ross ED. LCD-Composer: an intuitive, composition-centric method enabling the identification and detailed functional mapping of low-complexity domains. NAR Genom Bioinform 2021;3:lqab048. [PMID: 34056598 PMCID: PMC8153834 DOI: 10.1093/nargab/lqab048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/13/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]  Open
15
Moving beyond disease to function: Physiological roles for polyglutamine-rich sequences in cell decisions. Curr Opin Cell Biol 2021;69:120-126. [PMID: 33610098 DOI: 10.1016/j.ceb.2021.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/17/2022]
16
Hernandez R, Facelli JC. Structure analysis of the proteins associated with polyA repeat expansion disorders. J Biomol Struct Dyn 2021;40:5556-5565. [PMID: 33459170 PMCID: PMC8286276 DOI: 10.1080/07391102.2021.1871957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
17
Wang Y, Yang HJ, Harrison PM. The relationship between protein domains and homopeptides in the Plasmodium falciparum proteome. PeerJ 2020;8:e9940. [PMID: 33062426 PMCID: PMC7534687 DOI: 10.7717/peerj.9940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022]  Open
18
Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020;4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
19
Lobanov MY, Likhachev IV, Galzitskaya OV. Disordered Residues and Patterns in the Protein Data Bank. Molecules 2020;25:molecules25071522. [PMID: 32230759 PMCID: PMC7180803 DOI: 10.3390/molecules25071522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023]  Open
20
Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome. PLoS Comput Biol 2020;16:e1007487. [PMID: 31986130 PMCID: PMC7004392 DOI: 10.1371/journal.pcbi.1007487] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/06/2020] [Accepted: 12/23/2019] [Indexed: 11/29/2022]  Open
21
Galzitskaya OV, Novikov GS. An Overlap between Splicing Sites in RNA and Homo-Repeats in Human Proteins. Mol Biol 2019. [DOI: 10.1134/s0026893319030063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
22
Galzitskaya OV, Novikov GS, Dovidchenko NV, Lobanov MY. Is there codon usage bias for poly-Q stretches in the human proteome? J Bioinform Comput Biol 2019;17:1950010. [PMID: 30866735 DOI: 10.1142/s0219720019500100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
23
Galzitskaya OV, Lobanov MY. Proteome-scale understanding of relationship between homo-repeat enrichments and protein aggregation properties. PLoS One 2018;13:e0206941. [PMID: 30399196 PMCID: PMC6219797 DOI: 10.1371/journal.pone.0206941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]  Open
24
Cascarina SM, Ross ED. Proteome-scale relationships between local amino acid composition and protein fates and functions. PLoS Comput Biol 2018;14:e1006256. [PMID: 30248088 PMCID: PMC6171957 DOI: 10.1371/journal.pcbi.1006256] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/04/2018] [Accepted: 08/16/2018] [Indexed: 11/26/2022]  Open
25
Mier P, Andrade-Navarro MA. Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length. Genome Biol Evol 2018;10:816-825. [PMID: 29608721 PMCID: PMC5841385 DOI: 10.1093/gbe/evy046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2018] [Indexed: 12/16/2022]  Open
26
Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17. J Struct Biol 2017;201:162-170. [PMID: 29221897 DOI: 10.1016/j.jsb.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/08/2017] [Accepted: 12/04/2017] [Indexed: 11/20/2022]
27
Michel CJ, Ngoune VN, Poch O, Ripp R, Thompson JD. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae. Life (Basel) 2017;7:life7040052. [PMID: 29207500 PMCID: PMC5745565 DOI: 10.3390/life7040052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022]  Open
28
Mier P, Andrade-Navarro MA. dAPE: a web server to detect homorepeats and follow their evolution. Bioinformatics 2017;33:1221-1223. [PMID: 28031183 PMCID: PMC5408840 DOI: 10.1093/bioinformatics/btw790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/09/2016] [Indexed: 01/10/2023]  Open
29
Campbell L, Turner SR. A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. FRONTIERS IN PLANT SCIENCE 2017;8:37. [PMID: 28174582 PMCID: PMC5258720 DOI: 10.3389/fpls.2017.00037] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/09/2017] [Indexed: 05/20/2023]
30
Adaptive Variation and Introgression of a CONSTANS-Like Gene in North American Red Oaks. FORESTS 2016. [DOI: 10.3390/f8010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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