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PLAbDab Search

The PLAbDab (Patent and Literature Antibody Database) Search tool provides a list of sequences from the OPIG PLAbDab database that are similar to the selected entry.

This tool is essential for ensuring that a potential therapeutic candidate is unique and eligible for patent protection. Identifying sequences in the PLAbDab database that are similar to your selected antibody is a critical step in assessing freedom to operate and intellectual property (IP) risk. In the context of patent claims, sequence identity cutoffs often range from 80% to 95% for variable regions; sequences exceeding these thresholds may be blocked by existing IP rights. PLAbDab contains "over 150,000 paired antibody sequences derived from patents and academic papers".

Accessing the Tool

Select exactly one antibody in the Project View. Go to the Analysis menu and select PLAbDab Search. This will open the PLAbDab Search workspace in a new tab.

PLAbDab Search

Using the Tool

  • Max Hits: The maximum number of hits to display in the results table.
  • Search Regions: The regions to search for similar sequences. Default is all regions of the variable domains.
  • Run Comparison: Click this button to start the search.

The results table shows the following information:

  • Chain Tab: Select Light or Heavy to see its results.
  • Numbering: The numbering is shown in IMGT since that is the system used to process the sequence database.
  • Regions: The regions shown are North since that is the system used to process the sequence database.
  • Selected Entry: The sequence of the selected entry in ABHAND coloring.
  • Results Grid:
    • Source: The file type in which the hit was found. P for Paired Sequences or U for Unpaired Sequences.
    • Accession ID: The accession ID of the hit sequence. This is a clickable link which opens the entry in a new tab at NCBI.
    • LH: "LH" is shown if the hit is found for both the light and heavy chains.
    • % Identity: The percentage identity of the hit sequence to the selected sequence by IMGT position.
    • Identity Count: The number of identical over total residues between the hit sequence and the selected sequence.
    • Sequence: The sequence of the hit sequence with identical residues green and non-identical residues red.
  • Export Excel: Click this button to export the results table to an Excel file.

References

  • PLAbDab details are described in PLAbDab.