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

By Guangshun Wang, Xia Li, Zhe Wang. Nucleic Acids Res., 2008

946 citations recorded by the source corpus.

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.

Subfields: Microbiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1f0f73e74f660c958c58d685b0ee0e50c631e1d1

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Citations in the corpus

Antimicrobial peptides: key components of the innate immune system (2012, background): “Since then, more than 1400 AMPs have been isolated from bacteria, insects and other invertebrates, amphibians, birds, fishes, mammals, and plants (Wang and Wang, 2004; Wang et al., 2009a; Thomas et al., 2010).”
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides (2015, neutral): “These sequences are integrated in the Experimentally Val-idated or Predicted data set based on the annotation provided by APD2.”
BACTIBASE second release: a database and tool platform for bacteriocin characterization (2010, background): “The AMSDb (see: http://www.bbcm.univ.trieste.it/ ~tossi/amsdb.html), ANTIMIC [18], APD2 [19], and CAMP [20] databases cover all AMPs sequences from diverse origins.”
iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types. (2013, methodology): “constructed the antimicrobial peptide database (APD) [6] and the updated antimicrobial peptide database (APD2) [7], accessible at http://aps.”
In Silico Models for Designing and Discovering Novel Anticancer Peptides (2013, methodology): “Therefore, we have collected 225 experimentally validated ACPs from literature and from various databases 17–19 .”
Peptides: A Package for Data Mining of Antimicrobial Peptides (2015, background): “Additionally to these four properties there are other descriptors that used in conjunction can provide useful information in the classification and design of antimicrobial peptides (Boman, 2003; Wang et al., 2009; Thomas et al., 2010; Piotto et al., 2012).”
CancerPPD: a database of anticancer peptides and proteins (2014, background): “A few AMPs databases like Antimicrobial Peptide Database V2 (15), Collection of Antimicrobial Peptides Database (16) and Database of Anuran Defense Peptides (17) contain information on anticancer activities of some AMPs, however, the information related to ACPs is not comprehensive.”
MilkAMP: a comprehensive database of antimicrobial peptides of dairy origin (2014, background): “For example, APD and CAMP propose, respectively, one and four AMPs derived from lactoferrin.”
Designing antimicrobial peptides: form follows function (2011, background): “76) , is a valuable resource of AMP sequences.”
LAMP: A Database Linking Antimicrobial Peptides (2013, background): “There are 3,706 links to the CAMP and 1,972 links to the APD.”