Peptides

Import Peptides

In Marvin JS, it is possible to import peptide sequences by clicking the Import button, which is available on the General toolbar.

See the steps below for a detailed import process.

  1. Click the Import button on the General toolbar.

    images/download/attachments/13108370/Peptides_Imort_Button.png
  2. As the Import dialog opens you can start typing the 1- or 3-letter amino acid codes.

    images/download/attachments/13108370/Peptides_Imort_Dialog.png

    When importing, both 1- and 3-letter representations can be used, but Marvin JS always displays the amino acids by using their 3-letter forms on the canvas.

  3. When you finished entering the sequences press either Add or Replace. The Add button pastes the structures to the canvas, that is, all existing structures on the canvas are kept. On the other hand, the Replace button overwrites the existing structures on the canvas with the structure to be imported.

Drawing Disulfide Bridges

It is possible to draw disulfide bridges, to do so, simply select the Single Bond tool and click on a cysteine. Drag to cursor to another cysteine while holding the left mouse button. When the mouse button is released a new bridge will be created, crosslinking the two amino acids.

images/download/attachments/13108370/Peptides_Bridges.png

Drawing Cycles

To draw a head-to-tail cycle, delete the explicit H and OH from the terminal amino acids, then simply select the Single Bond tool and drag the cursor from the first amino acid to the last.

images/download/attachments/13108370/Peptides_Cycle.png

Specifying Attachment Points

When connecting two amino acids with multiple possible attachment points, you can specify the connection points through the Attachment Editor pop-up dialog.

The figures below show the two amino acids with different connection points.

images/download/attachments/13108370/Peptides_Attachment_Editor2_1.png

images/download/attachments/13108370/Peptides_Attachment_Editor2_3.png

images/download/attachments/13108370/Peptides_Canvas_Clean2_1.png

images/download/attachments/13108370/Peptides_Canvas_Clean2_3.png