Monomer Library

BioEddie ships with a pre-compiled small set of monomers, which can be extended using the built-in library manager. In addition BioEddie can be configured to use a monomer library that is maintained by the separate Biomolecule Toolkit product. The currently loaded library can be browsed and searched using the Library panel.

Monomers

Monomers with defined structure – PEPTIDE, RNA, CHEM

Monomers in BioEddie are defined by:

  • unique ID/abbreviation

  • name

  • type (PEPTIDE, RNA, CHEM)

  • functional type for RNA monomers (sugar, linker, base)

  • attachment R group(s) definition

  • natural Analogue (optional for PEPTIDE, RNA bases)

  • structure

This is compatible with HELM monomer specifications.

Currently max. 4 attachment points can be defined per monomer.

Monomers having no defined structure - BLOB

Blobs are characterized by:

  • unique ID/abbreviation

  • name

  • metadata

  • R group(s) definition (optional)

  1. If hidden, open the Library panel using the Panels drop-down menu on the toolbar

  2. Type a monomer name, abbreviation or monomer type into the search textbox

  3. Hover over to show a monomer preview displaying the structure, attachment points and leaving group definitions and monomer name

  4. Hit list ordered by relevance is displayed

Adding Ad hoc monomers

If you want to change the structure of your biomolecule, but there is no adequate monomer in the Monomer Library to do so, you can create an ad hoc modification of an existing monomer, which will not be saved in the library.

The structure will be kept as a temporary monomer in the library and can be used as a regular monomer for the duration of your current browser session.

Such monomers receive a generic abbreviation and will be displayed on the canvas with a dashed border.

  1. Double click on the monomer to be changed. MarvinJS is opened, displaying the original monomer structure.

  2. Change the structure.

  3. With any change to the structure you will be notified, whether the current structure is found as a monomer in the library or a new ad hoc modification will be created upon conforming the edited structure.

  4. By clicking "Done" the selected monomer gets replaced.

images/download/attachments/1806419/Change_monomer_MJS.png

New ad hoc modifications are preserved for the duration of your current browser session only. They will be saved as in-line SMILES when exporting your molecules in HELM format.