Designing AMPed: The Practical Antimicrobial Peptide Editable Database

Peptide data are stored in various online repositories. Researchers typically need to sift through numerous databases containing large quantities of unwanted information before locating the exact data they need. Routine access to vital data is a very complex and daunting challenge. Individual researchers, experimenting with innovative search and data filtering strategies, have built up their own local databases, adding to an ever-increasing volume of highly dispersed, partially overlapping, peptide datasets. None of the existing online databases uniformly annotates their data, making correlating entries for identical proteins or peptides from one dataset to another a staggering task. Bioinformaticians have developed software to simplify cross-database searching, but the problem of locating useful antimicrobial peptide research-related entries buried inside general databases remains. Presently, AMPed consists of data obtained by bulk downloads of proteins less than 100 residues from four large online portals: UniProt (www.uniprot.org), NCBI (www.ncbi.nlm.nih.gov), EBI (www.ebi.ac.uk), and KEGG (www.genome.jp).