dbAMP: Antimicrobial Database #

Introduction #

With the well-known general characteristics of antimicrobial peptides (AMP), which are highly effective in the mechanism of innate immune system to eradicate the pathogenic microbes. The intense knowledge is required about the AMP synthesis and its defense mechanism to identify the key factors to facilitate the next generation antibiotics to overcome the anti-biotic resistance pathogenic microbes. In this aspect, the collective knowledge is required to estimate the further directions, to fulfill this, the Tzong-Yi Lee et.al. established the antimicrobial database (dbAMP, http://csb.cse.yzu.edu.tw/dbAMP/), with the current state-of-art (Jhong et al., 2018). This database includes, 12,389 entries from eleven well known databases and content from 1924 research articles with the effective utilization of name entity recognition and natural language processing approach. Finally, this database also provides the standalone execution pipeline, which implemented in docker container, which facilitate the easy utilization of dbAMP to large scale projects.

Databases includes in dbAMP #

1) NCBI genbank 
2) Uniprot
3) Protein Data Bank (PDB)
4) APD3 
5) CAMPR3
6) ADAM
7) PhytAMP
8) AMPer
9) AntiBP2
10) BACTIBASE
11) LAMP

Content includes in dbAMP #

1) General sequence Information of the peptide 
2) Anti-microbial activities 
3) Post-translational modifications (PTMs)
4) Structural Visualization 
5) Anti-microbial potency
6) Targeted species with minimum inhibitory concentration (MIC)
7) Physiochemical properties 
8) AMP-protein interactions with the source references
9) Hemolytic activity (HC50)

Web-Applications #

1) Physiochemical properties calculation 
2) Random forest based AMP prediction for different species

Standalone pipeline #

The docker container named csbyzu/ismap can be used to identify the AMPs peptides from NGS reads and MS/MS-identified peptides.

Available dataset: #

There are species specific AMP test and training datasets available for seven group of taxonomy clades. i.e., Amphiabia, Bacteria, Fish, Human, Insects, Mammals and plants.

Reference #

1. Jhong, J.-H., Chi, Y.-H., Li, W.-C., Lin, T.-H., Huang, K.-Y., and Lee, T.-Y. (2018).
2. dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. Nucleic Acids Research, gky1030-gky1030.
3. doi: 10.1093/nar/gky1030.