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AMP facts and observations derived from the APD
AMP knowledge derived from the APD
The APD Hypothesis: We can design better peptide antibiotics if we understand nature's design principles of antimicrobial peptides. For this prupose, it is necessary to define a set of criteria for data registration (APD3).
Despite an increase in peptide count with time, a comparison of the database statistics between 2010 and 2020 reveals similar trends for amino acid signatures of bacteria, plants, insects, and amphibians (Wang et al., 2022).
For amino acid signatures from a vareity of natural AMP groups, you can refer to our publihsed papers (e.g., Wang, 2020). Go to the APD to view the most recent signatures.
For bioinformatic analysis of over 1000 amphibian AMPs, you can take a look at Wang (2020).
For a systematic analysis of amino acid-rich AMPs from the APD, you can read our recent paper Decker et al., 2022.
Please refer to the APD6 for an updated view on natural AMPs and their relationships with synthetic and AI predicted AMPs (limited to experiment-validated peptides).
References
1. Wang, G.*, Zietz, C.M, Mudgapalli, A., Wang, S., Wang, Z.(2022) The evolution of the antimicrobial peptide database over 18 years: Milestones and new features. Protein Science 31, 92-106. Read the article here
2. Wang, G.* (2013) Database-guided discovery of potent peptides to combat HIV-1 or superbugs. Pharmaceuticals 6, 728-758. Read the article here.
3. Mishra, B., Wang, G.* (2012). The importance of amino acid composition in natural antimicrobial peptides (AMPs): an evolutional, structural, and functional perspective. Frontier in Immunology 3, article 221. Read the article here.
4. Wang, G*, Li, X., Zasloff, M. (2010) A database view of naturally occurring antimicrobial peptides: nomenclature, classification and amino acid sequence analysis. In Wang, G. (ed.) "Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies". CABI, Oxfordshire, UK, pp. 1-21. Read the chapter here.
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