Sequence & Patent Scout β Walkthrough
How the scout works and every data source it queries β reference material for the main tool.
Get the sequence first
Full FASTA, VH/VL/CDR, SEQ ID, clone, and antigen sequence are the core assets; they matter even with no epitope yet.
Then read the epitope
If a patent explicitly claims an epitope, move to a claim chart and design-around; if not disclosed, back it out from structural and experimental clues.
Close the R&D loop
Form a target brief, design constraints, and a wet-lab validation plan, then write positive / negative results back as a reward signal.
API / data connector list
| Source | Priority | Use | Auth | Fields | Status | Docs |
|---|---|---|---|---|---|---|
| UniProt Antigen | P0 | Antigen resolution: sequence / gene / structure cross-refs (feeds epitope & structure search) | none | accession, recommended name, gene, length, sequence, PDB xref, function | live | open |
| AlphaFold Structure | P1 | Predicted antigen structure (recalled by accession; fills targets with no experimental structure) | none | entry id, model URL (PDB/CIF), mean pLDDT, confidence fractions, version, fragment | live | open |
| Europe PMC REST API | P0 | Public literature / bio-patent index recall | none | title, abstract, DOI, PMID/PMCID, year, source | live | open |
| NCBI E-utilities Patent Sequence | P0 | protein/nuccore patent sequence search | none | accession, patent sequence title, length, organism, patent number text | live | open |
| IEDB IQ-API | P1 | Known B-cell epitope evidence | none | epitope, antigen, receptor, pubmed, PDB | live | open |
| RCSB PDB APIs | P1 | Supplementary structural evidence | none | PDB ID, title, DOI, PubMed, method, resolution | live | open |
| The Lens Patent API | P0 | Primary patent API (integrated; runs when a token is configured) | LENS_API_TOKEN | patent metadata, family, legal status, claims, scholarly links | connected | open |
| Lens PatSeq / PatSeq Finder | P0 | Patent sequence library & BLAST-like sequence sourcing | Lens account / data access | patent sequence, SEQ ID, patent family, BLAST-like sequence hit | bulk | open |
| EPO OPS | P0 | Patent family / legal-status checks | OAuth consumer key/secret | bibliographic, full text, legal status, images | needs-key | open |
| WIPO PATENTSCOPE | P1 | PCT + sequence listing | web / SOAP data service | PCT publication, document, ST.25/ST.26 sequence listing | manual | open |
| WIPO sequence listings | P1 | PCT ST.25/ST.26 sequence-listing download & parsing | web / data product | sequence listing XML/TXT, sequence id, applicant, publication | manual | open |
| USPTO Open Data Portal | P1 | US file wrapper (prosecution history) | API key | application data, documents, office action, prosecution history | needs-key | open |
| SAbDab / Thera-SAbDab | P1 | Antibody structures / therapeutic antibody sequences | download / web | PDB structure, antibody chains, antigen, therapeutic sequence | bulk | open |
| ClinicalTrials.gov / FDA Purple Book | P2 | Therapeutic-antibody clinical / approval status | none / web | drug name, intervention, sponsor, trial phase, biologics listing | manual | open |