Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.
School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China.
Nucleic Acids Res. 2022 Jan 7;50(D1):D460-D470. doi: 10.1093/nar/gkab1080.
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.
在过去的 18 个月里，或者更长时间，我们的全球经历发生了深刻的变化，我们许多人都在应对百年一遇的大流行病。迄今为止，COVID-19 仍然是一种危及生命的大流行病，几乎没有针对性的治疗方法。新型抗病毒药物（如疫苗和药物）的发现可以为拯救人类免受严重感染提供治疗方案；然而，目前还没有专门针对 COVID-19 的有效抗病毒治疗方法。因此，人们非常关注使用天然或人工抗菌肽（AMPs），因为这些化合物被广泛认为是治疗有害微生物的有希望的解决方案。鉴于 AMPs 的生物学意义，显然需要一个单一的平台来识别和使用 AMP 数据。这导致了 dbAMP 平台的创建，该平台提供了有关 AMPs 的综合信息，并促进了它们的研究和分析。迄今为止，dbAMP 已经使用数据库集成和手动整理的超过 4579 篇文章，从 3044 个生物体中积累了 26447 种 AMPs 和 2262 种抗菌蛋白。此外，dbAMP 促进了使用 I-TASSER 对 AMP 结构进行评估，以进行自动蛋白质结构预测和基于结构的功能注释，为临床药物开发提供预测结构信息。下一代测序（NGS）和第三代测序已被用于从各种环境中生成大规模测序读数，从而大大提高了对基因组结构的分析能力。在本次更新中，我们推出了一个高效的在线工具，该工具可以在短时间内从所有物种的基因组/元基因组和蛋白质组数据中有效识别 AMPs。总之，这些改进推动了 dbAMP 成为 AMPs 最丰富和全面注释资源之一。更新后的 dbAMP 现在可以在 http://awi.cuhk.edu.cn/dbAMP 上免费访问。
