dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data

Jhih-Hua Jhong(Chinese University of Hong Kong, Shenzhen), Lantian Yao(Chinese University of Hong Kong, Shenzhen), Yuxuan Pang(Chinese University of Hong Kong, Shenzhen), Zhongyan Li(Chinese University of Hong Kong, Shenzhen), Chia‐Ru Chung(National Central University), Rulan Wang(Chinese University of Hong Kong, Shenzhen), Shangfu Li(Chinese University of Hong Kong, Shenzhen), Wenshuo Li(Chinese University of Hong Kong, Shenzhen), Mengqi Luo(Chinese University of Hong Kong, Shenzhen), Renfei Ma(Chinese University of Hong Kong, Shenzhen), Yuqi Huang(Chinese University of Hong Kong, Shenzhen), Xiaoning Zhu(Chinese University of Hong Kong, Shenzhen), Jiahong Zhang(Chinese University of Hong Kong, Shenzhen), Hexiang Feng(Chinese University of Hong Kong, Shenzhen), Qifan Cheng(Chinese University of Hong Kong, Shenzhen), Chunxuan Wang(Chinese University of Hong Kong, Shenzhen), Kun Xi(Chinese University of Hong Kong, Shenzhen), Li-Ching Wu(National Central University), Tzu‐Hao Chang(Taipei Medical University), Jorng‐Tzong Horng(National Central University), Lizhe Zhu(Chinese University of Hong Kong, Shenzhen), Ying‐Chih Chiang(Chinese University of Hong Kong, Shenzhen), Zhuo Wang(Chinese University of Hong Kong, Shenzhen), Tzong-Yi Lee(Chinese University of Hong Kong, Shenzhen)
Nucleic Acids Research
October 25, 2021
10.1093/nar/gkab1080
Cited by 179Open Access
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Abstract

The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.

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