The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
MODOMICS: a database of RNA modification pathways. 2021 update
Open accessAbstract
The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing and distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. Over the years, prompted by the accumulation of new knowledge and new types of data, it has been updated with new information and functionalities. In this new release, we have created a catalog of RNA modifications linked to human diseases, e.g., due to mutations in genes encoding modification enzymes. MODOMICS has been linked extensively to RCSB Protein Data Bank, and sequences of experimentally determined RNA structures with modified residues have been added. This expansion was accompanied by including nucleotide 5′-monophosphate residues. We redesigned the web interface and upgraded the database backend. In addition, a search engine for chemically similar modified residues has been included that can be queried by SMILES codes or by drawing chemical molecules. Finally, previously available datasets of modified residues, biosynthetic pathways, and RNA-modifying enzymes have been updated. Overall, we provide users with a new, enhanced, and restyled tool for research on RNA modification. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.
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Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1038 · Cited by 1,581 · cited 1×
“…nucleotide 5 - monophosphate residues to match the nucleoside counter-parts and sequences of experimentally determined RNA structures with modified residues have been added (an example illustrated in Figure 1), enabling MODOMICS to be linked to the RCSB Protein Data Bank database (rcsb.org) (22).”
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MODOMICS: a database of RNA modifications and related information. 2023 update
Cappannini, A., Ray, A., Purta, E., Mukherjee, S., Boccaletto, P., Moafinejad, S. N., Lechner, A., Barchet, C., Klaholz, B. P., Stefaniak, F., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1083 · Cited by 406
Self-citationBaek, A., Lee, G.-E., Golconda, S., Rayhan, A., Manganaris, A. A., Chen, S., Tirumuru, N., Yu, H., Kim, S., Kimmel, C., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01638-5 · Cited by 52
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Li, Q., Cheng, X., Song, C., & Liu, T. (2023) · Symmetry · doi:10.3390/sym15030731 · Cited by 20
Metadata
- Authors
- Boccaletto, P., Stefaniak, F., Ray, A., Cappannini, A., Mukherjee, S., Purta, E., Kurkowska, M., Shirvanizadeh, N., Destefanis, E., Groza, P., Avşar, G., Romitelli, A., Pir, P., Dassi, E., Conticello, S. G., Aguilo, F., & Bujnicki, J. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-12-06
- Volume
- 50
- Issue
- D1
- Pages
- D231-D235
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4200064844
- Cited by
- 813
- References
- 2
- FWCI
- 37.97
- Type
- journal article
- Language
- en
- Open access
- gold
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- The paper
- Boccaletto, P., Stefaniak, F., Ray, A., Cappannini, A., Mukherjee, S., Purta, E., Kurkowska, M., Shirvanizadeh, N., Destefanis, E., Groza, P., Avşar, G., Romitelli, A., Pir, P., Dassi, E., Conticello, S. G., Aguilo, F., & Bujnicki, J. M. (2022). MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab1083
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