Database Commons

a catalog of worldwide biological databases

Antimicrobial resistance is one of the most urgent global health threats, especially in the post-pandemic era. Antimicrobial peptides (AMPs) offer a promising alternative to traditional antibiotics, driving growing interest in recent years. dbAMP is a comprehensive database offering extensive annotations on AMPs, including sequence information, functional activity data, physicochemical properties and structural annotations. In this update, dbAMP has curated data from over 5200 publications, encompassing 33,065 AMPs and 2453 antimicrobial proteins from 3534 organisms. Additionally, dbAMP utilizes ESMFold to determine the three-dimensional structures of AMPs, providing over 30,000 structural annotations that facilitate structure-based functional insights for clinical drug development. Furthermore, dbAMP employs molecular docking techniques, providing over 100 docked complexes that contribute useful insights into the potential mechanisms of AMPs. The toxicity and stability of AMPs are critical factors in assessing their potential as clinical drugs. The updated dbAMP introduced an efficient tool for evaluating the hemolytic toxicity and half-life of AMPs, alongside an AMP optimization platform for designing AMPs with high antimicrobial activity, reduced toxicity and increased stability. The updated dbAMP is freely accessible at https://awi.cuhk.edu.cn/dbAMP/. Overall, dbAMP represents a comprehensive and essential resource for AMP analysis and design, poised to advance antimicrobial strategies in the post-pandemic era.

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.

Antimicrobial peptides (AMPs), naturally encoded from genes and generally contained 10-100 amino acids, are crucial components of the innate immune system and can protect the host from various pathogenic bacteria, as well as viruses. In recent years, the widespread use of antibiotics has inspired the rapid growth of antibiotic-resistant microorganisms that usually induce critical infection and pathogenesis. An increasing interest therefore was motivated to explore natural AMPs that enable the development of new antibiotics. With the potential of AMPs being as new drugs for multidrug-resistant pathogens, we were thus motivated to develop a database (dbAMP, http://csb.cse.yzu.edu.tw/dbAMP/) by accumulating comprehensive AMPs from public domain and manually curating literature. Currently in dbAMP there are 12 389 unique entries, including 4271 experimentally verified AMPs and 8118 putative AMPs along with their functional activities, supported by 1924 research articles. The advent of high-throughput biotechnologies, such as mass spectrometry and next-generation sequencing, has led us to further expand dbAMP as a database-assisted platform for providing comprehensively functional and physicochemical analyses for AMPs based on the large-scale transcriptome and proteome data. Significant improvements available in dbAMP include the information of AMP-protein interactions, antimicrobial potency analysis for 'cryptic' region detection, annotations of AMP target species, as well as AMP detection on transcriptome and proteome datasets. Additionally, a Docker container has been developed as a downloadable package for discovering known and novel AMPs on high-throughput omics data. The user-friendly visualization interfaces have been created to facilitate peptide searching, browsing, and sequence alignment against dbAMP entries. All the facilities integrated into dbAMP can promote the functional analyses of AMPs and the discovery of new antimicrobial drugs.