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APD specifications

Information


Unique identifier OMICS_05706
Name APD
Alternative name Antimicrobial Peptide Database
Restrictions to use None
Data access File download, Browse
Version 3.0
Maintained Yes

Publications for Antimicrobial Peptide Database

APD citations

 (27)
library_books

Large scale mapping of bioactive peptides in structural and sequence space

2018
PLoS One
PMCID: 5774755
PMID: 29351315
DOI: 10.1371/journal.pone.0191063

[…] ent of chronic disease []. In this sense, several databases and bioinformatics tools have been developed to predict and study BP occurrence in food proteins. Among the databases, we found PepBank [], Antimicrobial Peptide Database (APD) [] and BIOPEP []. Databases are the main source of information to predict occurrence of BP in proteins. Basically, primary structure information of characterized p […]

library_books

Selection strategy of phage displayed immunogens based on an in vitro evaluation of the Th1 response of PBMCs and their potential use as a vaccine against Leishmania infantum infection

2017
PMCID: 5740923
PMID: 29268793
DOI: 10.1186/s13071-017-2576-8

[…] ical properties of B1 and D11 phage-exposed peptides, such as molecular weight, hydrophobicity, and net charge were predicted, using the Compute pI/Mw tool (http://web.expasy.org/compute.pi/) and the antimicrobial peptide database server (http://aps.unmc.edu/AP/prediction/prediction main.php). […]

library_books

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

2017
PMCID: 5711939
PMID: 29214045
DOI: 10.1038/s41522-017-0042-1

[…] Prediction of AMP sequences within the identified ORFs was achieved using a variety of software available at various public databases. Specifically, we used the antimicrobial peptide database, the Antimicrobial Sequence Scanning System (AMPA), BACTIBASE, collection of anti-microbial peptides (CAMP),, and antibacterial peptides (AntiBP). Only ORFs that were pr […]

library_books

Multi label Learning for Predicting the Activities of Antimicrobial Peptides

2017
Sci Rep
PMCID: 5438384
PMID: 28526820
DOI: 10.1038/s41598-017-01986-9

[…] were considered and no existing multi-label learning methods were tested. To address these problems, firstly we constructed a new dataset with twelve biological activities covered based on the latest antimicrobial peptide database (APD) and a filtered dataset with only five activities covered but more biological significance; secondly, several previously described multi-label learning methods and […]

call_split

New Disulfide Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating Properties

2017
Toxins
PMCID: 5450702
PMID: 28468269
DOI: 10.3390/toxins9050154
call_split See protocol

[…] The BLAST search engine [], the Antimicrobial Peptide Database [], the InterProScan tool [] and StellaBase [] was used to search for homologues sequences. The SignalP4.1 server [] was used to predict the potential cleavage site of t […]

call_split

High Specific Selectivity and Membrane Active Mechanism of Synthetic Cationic Hybrid Antimicrobial Peptides Based on the Peptide FV7

2017
Int J Mol Sci
PMCID: 5343874
PMID: 28178190
DOI: 10.3390/ijms18020339
call_split See protocol

[…] The primary peptide physicochemical parameters and sequences were calculated using bioinformatics programs including ProtParam (ExPASy Proteomics Server) [] and the antimicrobial peptide database []. The secondary structure type of each residue was predicted online using Jpred 3 [] and I-TASSER []. […]

Citations

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APD institution(s)
Department of Pathology and Microbiology, University of Nebraska Medical Center, Nebraska Medical Center, Omaha, NE, USA
APD funding source(s)
NIH grant R01AI105147

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