Custom and Private Proteins

Custom and private proteins are both manually added proteins to 3DM Systems, but they differ in how they are defined and processed.

What are custom proteins

Custom proteins are sequences added to the 3DM system during system build, integrated into its superfamily alignment, and accessible to all users with system access. Optionally, a protein structure is linked to the custom protein sequence.

To view the custom proteins in a 3DM system, navigate to the custom protein page:
Sidebar → Proteins → Custom proteins

What are private proteins

Private proteins are protein sequences that are manually added after the 3DM system was build.
It is possible to add your own private proteins to a 3DM system. Any protein sequence that you wish to add manually is considered a private protein. Private proteins are projected onto the superfamily alignment and by default only visible to you, unless you choose to share them with specific user groups.

Private proteins can be connected to different 3DM systems. 

How do I add a private protein?

Private proteins can be created and/or connected to a 3DM system from the private protein page within a 3DM system. Navigate there via the sidebar:
Sidebar → Proteins → Private proteins.

Available functionality

The following features are available for private proteins:

• View them in the alignment.

• View private proteins in a phylogenetic tree of the 3DM system.

• Create structural models of private proteins connected to a 3DM system.

• Map 3DM data on the private protein sequence (see Protein analysis).

• Create a custom numbering scheme based on the private protein sequence.

Notes concerning private proteins:

• Private proteins are visible only to you or to the user group you share them with.

• 3DM data can be projected on private proteins but they themselves are not part of the statistics.

• It can be difficult to connect (align) distantly related proteins to a 3DM system (you are advised to check the alignment quality for such proteins).