dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data

Abstract

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.

In Silico Identification of Antimicrobial Peptides in the Proteomes of Goat and Sheep Milk and Feta Cheese

“…This suggests that the peptides resulting from milk digestion can potentially have a modulatory effect on the human gut microbiome profile [5,6]. Comparing the physicochemical properties (given in Supplemental Information) with those in several publicly available AMP databases, the selected AMP set in this work showed agreement with similar distributions reported in several databases containing experimentally validated AMPs, such as dbAMP [32], DBAASP [33], APD [34], CAMP [35] and LAMP [36]. The physicochemical properties were further evaluated by analysing the AMPs found in DBAASP, which contains the highest number of entries.…”

Antimicrobial Peptides as Potential Antiviral Factors in Insect Antiviral Immune Response

“…With increasing interest for natural AMPs as potential new drugs, many databases, such as APD ( 30 ), AVPdb ( 31 ) and ParaPep ( 32 ), have been developed to centralize information about AMPs. Among AMP databases, a few databases integrate the AMPs with antiviral activity such as APD ( 30 ), AVPdb ( 31 ), DRAMP 2.0 ( 33 ), and dbAMP ( 34 ). The information incorporated in DRAMP 2.0 and dbAMP is relatively new and complete.…”

“…The dbAMP was recently created as a useful resource for accumulating synthetic and natural AMPs from public AMP databases and scientific literature ( 34 ). In the dbAMP database, a total of 305 AVPs and 596 insect AMPs are collected ( Figure 1A ).…”

Potential Chimeric Peptides to Block the SARS-CoV-2 Spike RBD

“…In the second strategy, we screened the available antiviral peptides against the SARS-CoV-2 Spike RBD. We used Antiviral peptides database (AVPdb) [19], HIV inhibiting peptides database (HIPdb) [12], Antimicrobial peptide database (APD3) [20], dbAMP [21], and FDA approved therapeutic peptides and proteins database (THPdb) [22] and screened the peptides against the SARS-CoV-2 Spike RBD. In this process, the HPEPDOCK protein-peptide docking Server [18] was also used fixing the eight active amino acid binding sites of the Spike protein (Lys417, Tyr453, Gln474, Phe486, Gln493, Gln498, Thr500, and Asn501).…”