D-PeptideBuilder
User Guide
This is a concise guide that summarizes the main features of D-Peptide Builder.
Click here
to view a tutorial video.
Access the server
The server is hosted at
http://dpeptidebuilder.quimica.unam.mx:4000.
We suggest using Chrome or Firefox web browsers.
You will see the next home page.
Enumerate libraries
Fill out the form in home page.
 |
Step 1. Move the mouse over an "options" button,
choose desired options from
dropdown list.
Non-methylated: Select amino acid dataset.
N-Methylated: Select amino acid with N-Methylation.
Step 2. From dropdown list, select a single topology,
or both of them.
Step 3. Select a number between 2 and 5 to set the
peptide length.
Step 4. Click the “Submit” button to perform the
enumeration.
|
Enumerated libraries will show up in a new window, similar to the one at the next screenshot.
 |
Save database
Click “Download CSV” button,the database will be
downloaded as a .csv file.
Click “home” to return main page.
|
Visualization of chemical space
Select“Chemical Space” option on the side bar.
This section allows visualizing the chemical space by PCA and t-SNE using physicochemical properties and
Atom Pair fingerprints. Options are visualized in the next window:
Once desired choice is selected, click the button “Visualize”. An interactive plot
will be render in a new window.
 |
Toolbar include zoom in, zoom out and save options.
At legent section libraries hide and appear on click.
In the plot, placing the cursor in a single point,
coordinates and name
of a single
point are render on an alert window.
|
Note: To compare the chemical space of numerated data sets with other reference
libraries contact our group (medinajl@unam.mx or dieb@comunidad.unam.mx).
The full contact information is at
http://dpeptidebuilder.quimica.unam.mx:4000/contact.
Diversity Analysis
"Options" button displays the Atom Pair fingerprints. Similarity plot and statistical values will render in
a new window.