This tutorial provides step-by-step instructions for adding an antibody,
, to the Biologics registry.
Along the way it illustrates:
- Adding nucleotide sequences to the registry
- Options for translating protein sequences from the above
- Entity relationships
- The protein classification system which detects and annotates protein formats and components
- Calculated values for new sequences
This topic describes the manual process for adding a single entry to the registry. There are other options for adding entities, including bulk import options, importing GenBank files, and API-based insert methods.
Note that when you create your own entities, the registry names are auto-generated, and therefore may differ from the names shown in these tutorials.
Set Up Trial Server
- This tutorial assumes that you have registered and created a Biologics Trial instance of the server.
- If you have already created a biologics trial server, select it, and login: Your Sites
Register a Nucleotide Sequence
We register a sequence composed of a leader sequence + the light chain for Aducanumab.
- On the Biologics home page, click the Registry tile.
- On the Registry page, click Nucleotide Sequences.
- On the Nucleotide Sequences page, click Create and select Nucleotide Sequence.
- On the page Register a New Nucleotide Sequence, fill out the form as follows:
- Description: Copy and paste this text:
Signal Peptide 4 + Aducanumab Light Chain. The Light chain sequence of a IgG1 monoclonal antibody, which targets aggregated forms of β-amyloid (Aβ) in the hopes of reducing its buildup. Leader sequence HV103_HUMAN has been added.
- Alias: Add the two values below. Hit the Tab key to confirm each entry:
- Nucleotide Sequence Parents: Leave Blank
- Sequence: Copy and paste this sequence:
- Annotations: Leave Blank
- On the bottom right of the page, click Next.
- On the Confirm tab, review your entries and click Finish.
- Notice you could also translate a protein sequence immediately but to illustrate the two processes separately, just click Finish for now.
- The registry nucleotide sequence will be added to the registry. The name of the sequence (in these screenshots "NS-13") may be different in your registry, as the name is generated automatically. Once a new sequence is added, the registry enforces its uniqueness: if you attempt to register the same sequence twice, you will receive an error message.
Translate and Register a Protein Sequence
To translate a protein sequence based on this nucleotide sequence, follow the instructions below.
- On the Nucleotide Sequences page, click NS-13, or whatever the system has named your new nucleotide sequence.
- On the nucleotide sequence details page, select Create > Protein Sequences. (Note there are similar workflows available for Constructs and Vectors.)
- On the page Register a New Protein Sequence, enter the following information in the form:
- Description: Leave the automatically entered text unchanged.
- Protein Sequence Parents: Leave blank. (Use this when parent protein sequences are already in the registry.)
- Seq Part: Leave blank. (Use this when you know the sequence type, like Leader, Linker, or Tag.)
- Click Next.
- On the Sequence tab, click the dropdown Translation Frame and select "1". (Note that selecting "2" or "3" will re-render the sequence preview panes, as will manually refining the Protein Start and End points.)
- Click Next.
- The system searches the protein classification library and generates annotations for the sequence parts.
- Click Next on all remaining screens of the wizard. The wizard shows you calculated information on the following tabs:
- On the Annotations tab, review the information, and click Next.
- On the Properties tab, the system calculates a number of physical properties of the protein sequence. Review the information, and click Next.
- On the Confirm tab, click Finish.
- The new protein will be added to the registry. The auto-generated name of the new protein (in this case PS-27) may be different in your registry.
- Click the name of the new protein to see the details page. Under Related Entities, notice the link to the originating nucleotide sequence (NS-13).