BIOPEP-UWM* (www.uwm.edu.pl/biochemia) was developed in the Chair of Food Biochemistry of Warmia and Mazury University in Olsztyn (Poland). BIOPEP-UWM consists of the following integrated fundamental parts:
- sequence databases (proteins, bioactive peptides, allergenic proteins with their epitopes and sensory peptides including single amino acid residues);
- tools for the evaluation of protein as the precursors of bioactive peptides including the proteolytic processes design.
The all sequences gathered in the BIOPEP-UWM databases are inserted using the single letter code. Symbol “~” assigned to some peptide sequences means the C-terminal amide group. Such peptide appears in the BIOPEP-UWM twice: as the precursor with the Gly residue at the C-end and as the mature peptide. Such system allows to find the peptide in a protein precursor(s) (first case) or to identify it by mass spectrometry (second case).
All sequences available in BIOPEP-UWM posses the literature sources. In the case of proteins, Swiss-Prot (www.expasy.org) accession numbers are also provided. Sequences of peptides contain the measure of their bioactivity (EC50 value) if it is provided by literature resources.
Value of protein as the precursor of bioactive peptides can be estimated by following criteria:
- the profile of potential biological activity of protein;
- the frequency of the occurrence of bioactive fragments in a protein (A);
- the potential biological activity of protein (B).
Their definitions are available in the BIOPEP-UWM under the link “Definitions” and the above-mentioned parameters can be calculated clicking on the “Analysis”.
BIOPEP also provides the information what enzymes can release bioactive peptides (see the link “Enzymes action”). The proteolysis simulation is based on the recognition and cut sequence. First one is defined as the fragment of protein recognized by enzyme and the second one as the specific amino acid residues hydrolyzed by enzyme. It is possible to predict the bioactive products of an in silico hydrolysis of protein by selection from one to three endopeptidases with known specificity.
The links containing the words “…for your sequence” allow the user to evaluate the protein sequence which is not provided in the BIOPEP database by copying it from other resources and pasting to BIOPEP.
*To find out more information concerning BIOPEP-UWM see:
– “BIOPEP-UWM database of bioactive peptides: Current opportunities” by Minkiewicz P., Iwaniak A., Darewicz M. (Int. J. Mol. Sci., 2019, 20, 5978, doi: 10.3390/ijms20235978).
– “Biologically active peptides and food proteins — the health and nutritional aspects”. Dziuba J., Fornal Ł. (eds.), WNT Warszawa (in Polish).