The Repository of Amino Acids and Their Modifications—A Tool for Enlarging the Space of Food-Derived and Other Peptides in the BIOPEP-UWM Database

Abstract

Peptides are the most extensively studied bioactive compounds derived from food. They are analyzed using, e.g., in silico strategy. The BIOPEP-UWM database has become a standard tool in computer-aided peptide research. The aim of this study was to equip this database with a tool enabling the annotation and processing of peptide or protein sequences containing modified amino acid residues as well as other residues. The most recent section of the BIOPEP-UWM, i.e., the repository of amino acids and modifications, apart from 20 proteinogenic amino acids, annotates non-amino acid moieties or residues subjected to enzymatic or chemical modifications (phosphorylation, oxidation, hydroxylation, acylation, etc.). This part of BIOPEP-UWM provides the following information: Compound ID, name, symbol in a special code, InChIKey identifier, SMILES representation, number in the PubChem database (CID), formula, and IDs in other databases. The search options include ID in the repository, name, symbol in a biological code, InChIKey, PubChem Compound identifier (CID), and chemical formula. Peptide or protein sequences annotated using symbols from the repository are utilized by all applications available in the BIOPEP-UWM database. The database meets contemporary trends involving modifications of amino acid residues in the bioinformatic analysis of peptides and proteins.