APD2: the updated antimicrobial peptide database and its application in peptide design

The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/main.php) has been updated and expanded. It now hosts 1228 entries with 65 anticancer, 76 antiviral (53 anti-HIV), 327 antifungal and 944 antibacterial peptides. The second version of our database (APD2) allows users to search peptide f...

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Bibliographic Details
Published in:Nucleic acids research 2009-01, Vol.37 (suppl-1), p.D933-D937
Main Authors: Wang, Guangshun, Li, Xia, Wang, Zhe
Format: Article
Language:English
Subjects:
Animals
Anti-Infective Agents - chemistry
Anti-Infective Agents - pharmacology
Antimicrobial Cationic Peptides - chemistry
Antimicrobial Cationic Peptides - pharmacology
Antineoplastic Agents - chemistry
Antineoplastic Agents - pharmacology
Anura
Databases, Factual
Drug Design
Escherichia coli
Human immunodeficiency virus
Sequence Analysis, Protein
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Summary:The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/main.php) has been updated and expanded. It now hosts 1228 entries with 65 anticancer, 76 antiviral (53 anti-HIV), 327 antifungal and 944 antibacterial peptides. The second version of our database (APD2) allows users to search peptide families (e.g. bacteriocins, cyclotides, or defensins), peptide sources (e.g. fish, frogs or chicken), post-translationally modified peptides (e.g. amidation, oxidation, lipidation, glycosylation or d-amino acids), and peptide binding targets (e.g. membranes, proteins, DNA/RNA, LPS or sugars). Statistical analyses reveal that the frequently used amino acid residues (>10%) are Ala and Gly in bacterial peptides, Cys and Gly in plant peptides, Ala, Gly and Lys in insect peptides, and Leu, Ala, Gly and Lys in amphibian peptides. Using frequently occurring residues, we demonstrate database-aided peptide design in different ways. Among the three peptides designed, GLK-19 showed a higher activity against Escherichia coli than human LL-37.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkn823