Scenario 1
I want a dataset of both VHH and VNARs that bind to SARS-CoV-2.

Search PLAbDab-nano by keyword to find COVID-related single-domain antibodies using a regular expression: "SARS-CoV-2|COVID-19" ...

Returns the following results:

This shows a list of entries from different data sources that contain your keywords in their title. Only one entry will be shown per data source, but information from all entries can be downloaded using the "Download" link.

Clicking on the "Source URL" link will lead you to where the sequences were scraped from. More details on the antigen target can often be found there. Clicking on the ”More info” link will lead you to a page with more information on the selected entry.

The top of the "More info" page contains metadata for the selected entry, like the sequence, and the organism. For example:

For VHH entries, the predicted structure, modelled using NanoBodyBuilder2, can be viewed:

In the viewer, the structure can be represented using a selection of settings, such as cartoon (shown above), space-fill, ball & stick, or wire. To facilitate manual inspection of the VHH model, its structure can also be coloured by secondary structure, domains, or predicted error.

The bottom part of the page presents the user with options to download the structural model, or details on the retrieved VHH:

Scenario 2
You have a VHH, and you want to improve its properties by comparing its sequence and structure to patented and therapeutic single-domain antibodies that are similar.

To find these similar single-domain antibodies, we can search PLAbDab-nano using sequence identity or structural similarity. We will first search for entries with the highest average sequence identity over the whole sequence, above the specified cut-off (80%).

This returns 13 single-domain antibodies with sequence identities above our 80% cut-off:

Structure search

PLAbDab-nano can also be searched for VHHs with similar structures over the CDR loops. This may be useful for example where we want to maintain the structure of our query, but modify amino acids that may cause developability issues. We will search PLAbDab-nano for single-domain antibodies most similar (by lowest CDR RMSD) to a model of the query, below the specified cutoff (3Å).

This returns the following 10 entries:

We can see agreement between the results returned by the structure and sequence searches as well as additional entries included that may be useful to inform engineering strategies.

Contact

Feel free to contact us at opig <~at~> stats.ox.ac.uk with any issues or general enquiries about PLAbDab-nano.