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

Guangshun Wang, Xia Li, Zhe Wang

Research output: Contribution to journalArticle

627 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)D933-D937
JournalNucleic acids research
Volume37
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 9 2009

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Databases
Peptides
pamidronate
Cyclotides
Defensins
Amino Acids
Bacteriocins
Amphibians
Glycosylation
Anura
Antiviral Agents
Insects
Chickens
Membrane Proteins
Fishes
HIV
RNA
Escherichia coli
DNA

ASJC Scopus subject areas

  • Genetics

Cite this

APD2 : The updated antimicrobial peptide database and its application in peptide design. / Wang, Guangshun; Li, Xia; Wang, Zhe.

In: Nucleic acids research, Vol. 37, No. SUPPL. 1, 09.01.2009, p. D933-D937.

Research output: Contribution to journalArticle

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