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Li B, Yang S, Long J, Chen X, Zhang Q, Ning L, He B, Chen H, Huang J. AGODB: a comprehensive domain annotation database of argonaute proteins. Database (Oxford) 2022; 2022:6693399. [PMID: 36068786 PMCID: PMC9448894 DOI: 10.1093/database/baac078] [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: 01/03/2022] [Revised: 07/18/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
Argonaute (Ago) proteins are widely expressed in almost all organisms. Eukaryotic Ago (eAgo) proteins bind small RNA guides forming RNA-induced silencing complex that silence gene expression, and prokaryotic Ago (pAgo) proteins defend against invading nucleic acids via binding small RNAs or DNAs. pAgo proteins have shown great potential as a candidate ‘scissors’ for gene editing. Protein domains are fundamental units of protein structure, function and evolution; however, the domains of Ago proteins are not well annotated/curated currently. Therefore, full functional domain annotation of Ago proteins is urgently needed for researchers to understand the function and mechanism of Ago proteins. Herein, we constructed the first comprehensive domain annotation database of Ago proteins (AGODB). The database curates detailed information of 1902 Ago proteins, including 1095 eAgos and 807 pAgos. Especially for long pAgo proteins, all six domains are annotated and curated. Gene Ontology (GO) enrichment analysis revealed that Ago genes in different species were enriched in the following GO terms: biological processes (BPs), molecular function and cellular compartment. GO enrichment analysis results were integrated into AGODB, which provided insights into the BP that Ago genes may participate in. AGODB also allows users to search the database with a variety of options and download the search results. We believe that the AGODB will be a useful resource for understanding the function and domain components of Ago proteins. This database is expected to cater to the needs of scientific community dedicated to the research of Ago proteins.
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Affiliation(s)
- Bowen Li
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Shanshan Yang
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Jinjin Long
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Xue Chen
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Qianyue Zhang
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Lin Ning
- School of Health Care Technology, Chengdu Neusoft University , Chengdu, Sichuan 611844, China
| | - Bifang He
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Heng Chen
- Medical College, Guizhou University , Guiyang, Guizhou 550025, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China , Chengdu, Sichuan 611731, China
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He B, Yang S, Long J, Chen X, Zhang Q, Gao H, Chen H, Huang J. TUPDB: Target-Unrelated Peptide Data Bank. Interdiscip Sci 2021; 13:426-432. [PMID: 33993461 DOI: 10.1007/s12539-021-00436-5] [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: 12/21/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
The isolation of target-unrelated peptides (TUPs) through biopanning remains as a major problem of phage display selection experiments. These TUPs do not have any actual affinity toward targets of interest, which tend to be mistakenly identified as target-binding peptides. Therefore, an information portal for storing TUP data is urgently needed. Here, we present a TUP data bank (TUPDB), which is a comprehensive, manually curated database of approximately 73 experimentally verified TUPs and 1963 potential TUPs collected from TUPScan, the BDB database, and public research articles. The TUPScan tool has been integrated in TUPDB to facilitate TUP analysis. We believe that TUPDB can help identify and remove TUPs in future reports in the biopanning community. The database is of great importance to improving the quality of phage display-based epitope mapping and promoting the development of vaccines, diagnostics, and therapeutics. The TUPDB database is available at http://i.uestc.edu.cn/tupdb .
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Affiliation(s)
- Bifang He
- School of Medicine, Guizhou University, Guiyang, 550025, China. .,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - Shanshan Yang
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Jinjin Long
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Xue Chen
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Qianyue Zhang
- School of Medicine, Guizhou University, Guiyang, 550025, China
| | - Hui Gao
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Heng Chen
- School of Medicine, Guizhou University, Guiyang, 550025, China.
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 611731, China.
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