AI Patent Prosecution for Pharma & Biotech: Chemical Structures, Sequence Listings, and Markush Groups
How AI handles the unique challenges of pharmaceutical and biotechnology patent prosecution -- and where human expertise remains critical.
Why Pharma Patents Are Different
Pharmaceutical and biotechnology patents present unique challenges that general-purpose patent AI tools often fail to handle. Chemical structures cannot be described in plain text. Sequence listings follow specific WIPO standards. Markush groups define genus claims that require careful written description analysis. And 101 eligibility for diagnostic methods and natural products remains one of the most complex areas of patent law.
SMILES, InChI, and structural formula parsing in claim elements
WIPO ST.26 XML format, nucleotide and amino acid sequences
Genus/species claim analysis with variable group permutations
Natural product, diagnostic method, and abstract idea challenges
How Abigail Handles Pharma-Specific Challenges
Chemical Structure Analysis
Abigail parses chemical structures referenced in Office Actions and maps them against claim elements. The system recognizes SMILES notation, common chemical nomenclature, and structural descriptions in prior art citations.
- Identifies structural similarities and differences between claimed compounds and prior art
- Maps substituent groups to Markush variable positions
- Flags potential 103 combinations based on structural analogy
Sequence Listing Support (WIPO ST.26)
The platform handles WIPO ST.26 XML sequence listings that became mandatory in 2022. Sequence-dependent claims receive specialized analysis through the 10-expert pipeline.
- Parses nucleotide and amino acid sequences from claim text
- Identifies sequence identity percentages cited in rejections
- Maps sequence variants to species/genus claim relationships
Markush Group and Genus Claim Analysis
Markush groups and genus claims are a hallmark of pharmaceutical patents. Abigail identifies the variable positions, maps prior art to specific species within the genus, and flags written description concerns for broad genus claims.
- Parses Markush variable groups and permutations
- Identifies species anticipation within genus claims
- Flags 112(a) written description issues for genus claims
Where Human Expertise Remains Critical
AI excels at extraction, mapping, and pattern recognition. But pharma patent prosecution has areas where attorney judgment is irreplaceable:
- Terminal disclaimer strategy for double patenting (risk/benefit analysis across patent families)
- Patent term adjustment and patent term extension calculations
- Orange Book listing strategy and Hatch-Waxman considerations
- Prosecution history estoppel implications of specific amendment language
- Continuation/divisional strategy for portfolio management
- 101 subject matter eligibility arguments for diagnostic methods and natural products
Test With a Pharma Office Action
Upload a pharmaceutical or biotech Office Action and see how the 10-expert pipeline handles chemical structures and sequence-dependent claims.