MBPDB: Help
This function is for searching a single peptide or batch of peptides towards the bioactive peptides in the MBPDB database. Several search options are available and they can be used individually or in combination.
Input a single amino acid sequence of you peptide such as ‘ENLLRFFVAPFPEVFG’ or upload a file with multiple peptide sequences. This should be a text file with one column for the text files, which you can prepare in e.g. notepad.
Tip: You can also input part of a protein sequence to identify bioactive peptides in that region of the protein. To do this you would have to select precursor in the sequence search options.
Select a search option of your desire. The search functions are based on the protein blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins) search algorithm.
Matches the entire input amino acid sequence to all database entries and returns matches that has a similarity threshold equal or higher than the threshold value set.
Searches for any of the bioactive database entries containing the input amino acid sequence with an equal or higher similarity than the set similarity threshold. The input amino acid sequence is indicated with bold text in the result sequences.
Searches for bioactive peptides within the database which is contained within the input amino acid sequence with equal or higher similarity than the set similarity threshold.
This option allows for searching database entries with similarities to the input single peptide sequence. The search is based on a scoring matrix which is either identity or BLOSUM62. A restriction of the similarity search is that the peptides is at least four amino acids long. Sequences below four amino acids will automatically only search sequences that has a 100% similarity even though the indicated value is set lower than this.
The scoring matrix assigns an alignment score for all pair of amino acid residue matches to calculate the % similarity between the input amino acid sequence and database entries. Currently the database contains the identity and BLOSUM62 scoring matrix.
This scoring matrix is based on exact pairwise amino acid residues matches.
The BLOSUM62 scoring matrix uses an amino acid substitution matrix for the alignment score of all pairs of amino acid residue matches to calculate the % similarity (Figure 1).
Figure 1: BLOSUM62 substitution matrix (Henikoff & Henikoff, 1992).
This function provides additional information on the subject and query match obtained by protein blast and does not work for peptides below four amino acids long. The additional information obtained for each match are: % alignment, query and subject start and stop position, e-value, alignment length, mismatches and gaps.
Searches for bioactive peptides derived from a specific protein. Input the protein ID also known as protein entry on uniprot.org. For example, bovine beta casein has protein ID ‘P02666’. If the protein ID is not present in the database, it can be added in fasta file format through the MBPDB add proteins function. Through this function it is also possible to add genetic variants of a protein and assigning it a new protein ID.
Searches for bioactive peptides with a specific function. Write your own or select from the dropdown menu (ACE-inhibitory, antimicrobial, DPP-IV-inhibitory, Antioxidant, Immunodmodulatory or Antinflammatory).
The search result can be downloaded as a Tab-separated values file by checking this box and opened using e.g. Microsoft excel.
Search MBPDB for multiple peptides with different search terms using this function. Use a correctly formatted TSV (tab-separated values) file with UTF-8 encoding for uploading. We suggest you download the example file and use that as a template for preparing your own file.
Note that the Peptide Sequence, Protein ID, Function, Species, and Category columns can be empty. Also, if peptide is empty, search_type, similarity_threshold, scoring_matrix, and extra_output will be ignored.
This function is for adding a single entry into the database. Before the entry is added, it needs to be accepted by a database administrator.
Input the single letter amino acid sequence of you peptide of the bioactive peptide.
Add the category that the bioactive peptide belongs to. This could be Dairy, Cheese, casein etc. Note that this is optional.
Input the protein ID of the protein from where the bioactive peptide derives. This is similar to the entry identifier for protein in uniprot.org, e.g. P02666 for bovine beta-casein and is a unique ID for each known protein. The input peptides sequence has to match a sequence in the protein ID, otherwise the database will not accept the entry. The database will automatically identify the species based on the protein ID, and stored information about the peptides sequence start and stop position in the protein. In case of a genetic variant of a protein, add the genetic variant as a new protein in fasta format through the MBPDB add proteins function. Use the newly inputted protein ID for the genetic variant in this field afterward.
Input the function of the bioactive peptide you wish to add to the database. Write your own or select from the dropdown menu (ACE-inhibitory, antimicrobial, DPP-IV-inhibitory, Antioxidant, Immunodmodulatory or Antinflammatory).
Add the additional function information in this field in connection to the function added. This field is often used to add information on the activity level and assay conditions of the function given in the previous field. If you peptide is ACE-inhibitory, then added the activity. Note that this field is optional but highly recommended.
Example:
If you peptide is ACE-inhibitory and used the assay described by Cushman and Cheung (1971), then your secondary function field should state the activity and assay information: 182 μM, Cushman and Cheung (1971).
Input the title of the paper published describing the bioactivity.
Input the authors of the paper published describing the bioactivity.
Input the abstract of the paper published describing the bioactivity. Note this is optional.
Input the DOI of the paper published describing the bioactivity or Patent no. of the patented peptide. If this information is not available, input N/A.
This function is for adding multiple entries into the database by uploading the information as a .tsv file. Use a correctly formatted TSV file with UTF-8 encoding. We suggest your download the example file on the homepage and use this one to prepare your data. An example is shown below. The data required are similar as those for the MBPDB add single entry. Before the entry is added, it needs to be accepted by a database administrator.
This function is made for adding protein information into the database in fasta format (example shown below). Select one or multiple fasta files to be uploaded and press run. This function should be used when adding entries to the database which gives the error that the Protein ID is not in the database. This function could also be used to add genetic variant of proteins by adding their sequence information in fasta format. Several proteins are milk proteins are already added to the database and can be view through the “View current protein fasta headers (IDs)” link.
References:
Henikoff S, Henikoff J.G. 1992. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992 Nov 15; 89(22): 10915–10919.