MODOMICS: a database of RNA modification pathways. 2021 update.
MODOMICS: a database of RNA modification pathways. 2021 update.
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MODOMICS：RNA修饰途径数据库。2021年更新。
DOI：
10.1093/nar/gkab1083
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发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Bujnicki JM
中科院分区：
文献类型：
--
作者：
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 SG;Aguilo F;Bujnicki JM
自2006年以来，MODOMICS数据库一直是一个人工管理和集中的资源，存储和分发有关修饰核糖核苷的全面信息。最初，它只包含修饰的核糖核苷的化学结构，它们的生物合成途径，修饰的残基在RNA序列中的位置和RNA修饰酶的数据。多年来，由于新知识和新类型数据的积累，该系统不断更新，增加了新的信息和功能。在这个新版本中，我们创建了一个与人类疾病相关的RNA修饰目录，例如，这是由于编码修饰酶的基因发生突变。MODOMICS已广泛链接到RCSB蛋白质数据库，并添加了实验确定的具有修饰残基的RNA结构的序列。这种扩增伴随着包括核苷酸5′-单磷酸残基。我们重新设计了Web界面，并升级了数据库后端。此外，还包括一个化学相似的修饰残基搜索引擎，可通过SMILES代码或绘制化学分子进行查询。最后，以前可用的数据集修改的残留物，生物合成途径，和RNA修饰酶已更新。总的来说，我们为用户提供了一个新的，增强的和重新设计的工具，用于研究RNA修饰。MODOMICS可在https://iimcb.genesilico.pl/modomics/上获得。
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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影响因子：
3.5
作者：
Schaefer MR
通讯作者：
Schaefer MR
影响因子：
8.6
作者：
Bienfait B;Ertl P
通讯作者：
Ertl P
DOI：
10.1261/rna.067033.118
发表时间：
2018-10
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Wang X;Matuszek Z;Huang Y;Parisien M;Dai Q;Clark W;Schwartz MH;Pan T
通讯作者：
Pan T
影响因子：
5.1
作者：
Kumari K;Groza P;Aguilo F
通讯作者：
Aguilo F
影响因子：
4.5
作者：
Shelton SB;Reinsborough C;Xhemalce B
通讯作者：
Xhemalce B