Data collection
Data on the AMPs and EOs were collected from various sources. For the EOs, information was collected from scientific literature focusing on specialized peer-reviewed journals, through an advanced search of PubMed. Data on active AMPs were mainly extracted from public databases such as “The Antimicrobial Peptide Database” (APD) (http://aps.unmc.edu/AP/main.html) (Wang et al. 2008), (YADAMP) (http://www.yadamp.unisa.it/) (Piotto et al. 2012) and UniProt (http://www.uniprot.org/). All data entries were then manually curated. In addition, we used the Scientific Database Maker software SciDBMaker (Hammami et al. 2008) a new tool for protein data analysis, to calculate physicochemical profiles for loaded proteins such as amino acid composition (acidic, basic, hydrophobic, polar, and common amino acids), atomic composition, molecular weight, theoretical pI, extinction coefficient, absorbance at 280 nm, estimated half-life in mammalian cells, yeast and Escherichia coli, instability index, aliphatic index, grand average of hydropathicity (GRAVY) and protein-binding potential (Boman index) (Hammami et al. 2008).
Web interface and application
ANTIPSEUDOBASE runs on a Linux platform with the Apache webserver (2.4.7), MySql server (8.0.25-0ubuntu0.20.04.1), and PHP (7.4.3). For the development of this application, we used R-shiny as a programming language. We also usedseveral R packages includingggplot2, shiny, dplyr, proper, and DT.
This application and the database are hosted at http://bims.pasteur.tn:3838/APP/
The main page of the database contains the following interfaces: about EOs, AMPs and their activities against P. aeruginosa (introduction), general information (with query interface), physicochemical data (with query interface), links, and contact information.
Data extraction and query interface
The main page of the database contains the following interfaces: about EOs, AMPs, and their activities against anti-P. aeruginosa (introduction), general information (with query interface), physicochemical data (with query interface), literature data (with query interface), links, and contact information. The query interface provides search with a variety of parameters. The web interface of ANTIPSEUDOBASE is designed to offer a simple but practical use of the database. It is possible to query the database by peptide general data (ANTIPSEUDOBASE ID, producer organism, target organism), physicochemical data (ANTIPSEUDOBASE ID, producer organism, target organism name, mass, net charge), literature data (author, title, journal) and essential oils (ANTIPSEUDOBASE ID, major component essential oil, producer plant, reference). Any query can be made by combining as many fields as the user likes.
It is possible to make a query to select peptides with a similar name in this case (brevinin) and producer organism (Rana pirica). Selection of peptides produced by (Rana pirica) and with (brevinin) name recovers 3 sequences for further investigation (Figure 1). Selection of (synthetic) peptides with (length > 5 amino acids) recover 6 sequences for further investigation (Figure 2).
Database content
The ANTIPSEUDOBASE contains two types of anti-P. aeruginosa molecules, the peptides, and the EOs. For each entry, a unique three-digit identification number (ID) starting with the prefix ‘antipseudo’ was assigned. For the peptides, the data base contains general data such as peptide name, sequence, producer organism, target organism, and minimum inhibitory concentration (MIC) value. The physicochemical dataset was designed using SciDBMaker (Hammami et al. 2008) including empirical formula, mass, length, isoelectric point, net charge, basic, acidic, hydrophobic and polar residues, absent amino acids, binding potential index, instability index, aliphatic index, half-life in mammalian cells, yeast and E. coli, extinction coefficient, absorbance at 280 nm and their composition in term of amino acids. For EOs, each entry contains general data such as major components of the EO, percentage, origin plant, location, target organism, and reference including links to the abstract of original papers for further reading.