UserGuide For FeptideDB

User Guide
Peptide Search
FeptideDB was originated with two functions of preferences, including

‘search by sequence’ and ‘search by BPs activity’.
1. Submit query protein sequences in FASTA format.
2. Select the search by activity or default parameter.
3. Press submit data when form is completed, or use the reset button for
clearing data.
4. Users can download results by choosing “Export results”.

How to access results
Users can download results by choosing “Export results” to obtain the

result_file.txt.
This result_file.txt is saved in table format, which includes the following
data: ID (coding item in our database), peptide sequence, length, no.
peptide on protein, position, name, function, activity, CHEMMASS,
MONOMASS and EC50. This file can be opened by any worksheet
program.
Enzyme digestion
Digestion with enzyme
PDB File
Bioactive peptides
This module provides an in silico enzyme digestion to simulate bioactive

peptides cleaved from query protein sequences via two cleavage options.
The dataset of 15 restriction enzymes is based on the PeptideCutter tool
(https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html).
1. Submit input protein sequences in FASTA format.
2. Select the enzyme by default parameter (Automatics). The FeptideDB

allows automatic enzyme mode combination or two cleavage options.
3. Results in exact matches of cleaved peptide fragments derived from

food protein and BPs in BP fragments containing 2-10 residues length are
automatically generated using the FeptideDB-3D structure prediction tool
by choosing “PDB”.
*Construction of PDB file(s) have been provided for only 2-10 AA

peptides.
Users can either (A) view results of each enzyme and obtain a new pop-
up window or (B) download the summarized file by choosing “Export
results” and obtain the result_file.txt.
B
A
A view: Results of in silico enzyme digestion are displayed in the pop-up
window. BP fragments containing 2-10 residues are automatically
generated with the FeptideDB-3D structure prediction tool. These
constructed structures are written out and are available to download in
PDB file format.
B Export results: This result_file.txt is saved in table format, which
contains the following data: type of enzyme, digested peptide, position of
cleavage, activity group, number of digested peptide and score. This file
can be opened by any worksheet program.
Protein-ligand docking
FeptideDB predicts a new potential inhibitor against the target protein,

Angiotensin-I converting enzyme (ACE), using a molecular docking
approach. This module is named B-AceP, which is a platform to assist
users in obtaining images of the ACE-peptide interactions online. This
tool already provides input structures ready for docking the ACE protein
(PDB 1O86). Users can upload ligand files (pdb format) and perform
docking studies online. The ACE-ligand docking will be computed on
servers by the Autodock 4.2 program (http://autodock.scripps.edu/).
1. Upload ligand* file only in PDB format, which contains only 2 to 4
amino acid residues.
2. Press PROCESS LIGAND to submit the job. Do not close this window
during processing. It will take time for computing (5 to 30 minutes
depending on the internet speed and the computing queue in the
server).
3. The docked results file provides several formats, including 1) the ACE-
protein file, 2) lowest energy ligand file and 3) docked-log (dlg) file.
Docked results will be available once the computing finishes. The

docked results file provides several formats, including 1) the ACE-
protein file, 2) lowest energy ligand file and 3) docked-log (dlg) file.
An example of docked-log (dlg) file visualized in the Text-editor
program.
Further information about reading dlg file can be found at the following
links: http://autodock.scripps.edu/faqs-help/faq
http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-
protein-ligand-complex-as-a-pdb-file-in-autodock

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User Guide

FeptideDB was originated with two functions of preferences, including

1. Submit query protein sequences in FASTA format.

2. Select the search by activity or default parameter.

4. Users can download results by choosing “Export results”.

Users can download results by choosing “Export results” to obtain the

This module provides an in silico enzyme digestion to simulate bioactive

1. Submit input protein sequences in FASTA format.

2. Select the enzyme by default parameter (Automatics). The FeptideDB

3. Results in exact matches of cleaved peptide fragments derived from

*Construction of PDB file(s) have been provided for only 2-10 AA

FeptideDB predicts a new potential inhibitor against the target protein,

How to access results

Docked results will be available once the computing finishes. The

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