TY - JOUR
T1 - dbAMP 2.0
T2 - Updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data
AU - Jhong, Jhih Hua
AU - Yao, Lantian
AU - Pang, Yuxuan
AU - Li, Zhongyan
AU - Chung, Chia Ru
AU - Wang, Rulan
AU - Li, Shangfu
AU - Li, Wenshuo
AU - Luo, Mengqi
AU - Ma, Renfei
AU - Huang, Yuqi
AU - Zhu, Xiaoning
AU - Zhang, Jiahong
AU - Feng, Hexiang
AU - Cheng, Qifan
AU - Wang, Chunxuan
AU - Xi, Kun
AU - Wu, Li Ching
AU - Chang, Tzu Hao
AU - Horng, Jorng Tzong
AU - Zhu, Lizhe
AU - Chiang, Ying Chih
AU - Wang, Zhuo
AU - Lee, Tzong Yi
N1 - Publisher Copyright:
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/)
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85123389271&partnerID=8YFLogxK
U2 - 10.1093/nar/gkab1080
DO - 10.1093/nar/gkab1080
M3 - Article
C2 - 34850155
AN - SCOPUS:85123389271
SN - 0305-1048
VL - 50
SP - D460-D470
JO - Nucleic acids research
JF - Nucleic acids research
IS - 1
ER -
