Low-identity structural scaffolds, pre-filing sequence audits, and SPPS miniproteins.
Built for biotech R&D teams and patent prosecution counsel: discover functional 3D homologs and ancestral nodes far outside crowded sequence-identity claims, verify genus claim math and WIPO ST.26 XML listings before filing, or mine compact peptides and knottins sized for chemical synthesis.
Source active-site-conserved 3D homologs and ancestral nodes at <25% identity.
Standard BLAST searches saturate above 30% sequence identity and miss repetitive or compositionally biased scaffolds due to default low-complexity masking. We combine 3D structural pocket retrieval, unmasked alignment, and maximum-likelihood ancestral sequence reconstruction (ASR) to deliver a diversity-compressed synthesis plate accompanied by a factual sequence- and structure-similarity matrix for your patent counsel’s review.
01 · You Provide
- Query enzyme, binder, or structural protein (FASTA or PDB/mmCIF) and required catalytic/cofactor residues.
- Reference patent or public sequences whose global/domain percent-identity thresholds you want tabulated.
- Target plate size (24, 48, or 96 wells) and operating temperature/pH regime.
02 · Computational Protocol
- 3D structural & unmasked search: retrieves distant fold homologs across public metagenomic and genomic structures while disabling masking filters that drop repeat proteins.
- Ancestral sequence reconstruction: infers high-posterior internal nodes across outgroup clades, routinely raising thermostability while shifting global identity away from modern patented species.
- Pairwise identity & TM-score audit: computes global Needleman-Wunsch, domain-local, and 3D TM-score tables against every reference sequence.
03 · Deliverable Package
- Diversity-compressed 24/48/96-well candidate FASTA panel + refolded 3D PDB models verifying active-site closure.
- Counsel-ready CSV/PDF comparison matrix (technical data only; legal FTO opinions remain with registered patent counsel).
- Related reading: Default sequence masking hides repeat homologs →
| Package Tier | Discovery & Reconstruction Scope | Turnaround | Fixed Fee | |
|---|---|---|---|---|
| 3D Homolog Search + Plate Panel | 3D structural + unmasked metagenomic retrieval, active-site 3D filtering, diversity compression & reference %ID matrix | 7 business days | $6,000 – $9,500 | Select tier → |
| Full 3D Search + Ancestral Reconstruction (ASR) | Full 3D homolog discovery + maximum-likelihood phylogenetic tree, posterior ancestral node reconstruction & 3D refolding | 7–10 business days | $10,000 – $14,000 | Select tier → |
Catch mathematical claim contradictions, public collisions, and ST.26 errors before filing.
Designed for patent attorneys, patent agents, and biotech IP teams prior to provisional, PCT, or non-provisional filing. Sequence claims routinely ship with impossible percent-identity + motif combinations, signal-peptide residue-numbering offsets between claims and specification, prokaryotic GTG/TTG start-codon mistranslations, or unmasked public database hits inside an overbroad 70%–80% identity floor.
01 · You Provide
- Draft claims, specification residue tables, and candidate FASTA or WIPO ST.26 XML file (under mutual NDA / counsel-directed confidentiality).
- Key species or embodiment sequences that every independent and dependent claim is intended to cover.
02 · Computational Protocol
- Claim scope & embodiment coverage check: verifies mathematically that every claimed SEQ ID NO, motif, length bound, and percent-identity floor actually covers your lead variants without impossible intersections.
- Unmasked public collision sweep: searches every claimed sequence with low-complexity masking disabled to find the closest public natural sequence and establish safe fallback %ID floors.
- Numbering & WIPO ST.26 XML audit: verifies precursor vs. mature residue indices, genetic-code tables, and schema compliance.
03 · Deliverable Package
- Line-by-line technical discrepancy & collision ledger for counsel review prior to filing or conversion.
- Validated WIPO ST.26 XML check log + exact pairwise alignment appendices.
- Related reading: Four sequence-math bugs in biotech patent filings →
| Package Tier | Sequence Listing & Docket Scope | Turnaround | Fixed Fee | |
|---|---|---|---|---|
| Single Filing Audit DB-SVC-07-SINGLE | Up to 50 SEQ ID NOs; claim math satisfiability, unmasked public collision table, numbering offset & ST.26 QC | 2–3 business days | $4,500 – $6,000 | Select tier → |
| Large Listing / Multi-Docket DB-SVC-07-LARGE | 51 to 250+ SEQ ID NOs or multi-family diligence portfolio audit | 3–4 business days | $6,500 – $9,500 | Select tier → |
| Patent Counsel Pre-Filing 4-Pack DB-PACK-07-4AUDIT | Four single-filing audits (≤50 SEQ ID NOs each, $3,500/audit) usable across client dockets over 12 months with 48h priority | 2–3 business days | $14,000 upfront | Select pack → |
SPPS-ready peptides, 6-Cys knottin grafts, and short homo-oligomers (8–110 aa).
When full-length biologics are too large, protease-sensitive, or expensive to formulate, compact 8–110 residue scaffolds enable direct solid-phase peptide synthesis (SPPS), native chemical ligation (NCL), or compact single-AAV delivery. We excise self-folding bioactive segments, graft target loops onto protease-resistant cystine-knot scaffolds, and design short peptide oligomers that assemble functional pockets across chains.
01 · You Provide
- Target interface, bioactive motif, metal ion, or parent protein from which you want an SPPS-sized peptide excised.
- Manufacturing route & length ceiling (e.g., ≤50 aa single-shot Fmoc SPPS, ≤90 aa NCL, or single-AAV cassette).
- Formulation constraints (pH, serum/gut proteases, oxidation tolerance).
02 · Computational Protocol
- Peptide excision & knottin grafting: isolates self-folding peptide segments or grafts target motifs into 3-disulfide cystine-knot scaffolds verified by template-free 3D folding.
- Short self-assembling oligomer screening: evaluates symmetric C2–C6 peptide oligomers while filtering out cross-β aggregation and amyloid false positives.
- SPPS manufacturability audit: flags difficult coupling stretches, aspartimide motifs, Met/Trp oxidation sites, and NCL ligation junctions.
03 · Deliverable Package
- Diversity-compressed SPPS or gene-fragment order sheet (12–48 candidates) with 3D PDB monomer/oligomer coordinates.
- SPPS coupling-difficulty, disulfide-connectivity, and protease-clip scorecard.
- Pairwise sequence-identity matrix against public databases and reference patents.
| Package Tier | Peptide / Miniprotein Scope | Turnaround | Fixed Fee | |
|---|---|---|---|---|
| Bioactive Peptide Excision or Knottin Loop Grafting | Self-folding 8–65 aa peptide mining or 6-Cys cystine-knot loop grafting + SPPS manufacturability & 3D folding check | 7–10 business days | $10,000 – $14,000 | Select tier → |
| Short Self-Assembling Peptide Oligomers (≤110 aa) | Symmetric homo-oligomer discovery assembling inter-chain catalytic pockets or metal-binding cages + explicit-water MD | 8–10 business days | $14,000 – $18,000 | Select tier → |
Continue across the computational R&D lifecycle.
Protein Triage & Sequence Optimization
300 K / 330 K explicit-solvent MD triage and active-site-locked sequence liability scrubbing.
Construct Design & Clone Verification
Contingent repetitive gene synthesis rescue, raw-read broken gene reconstruction, and Nanopore/HiFi clone integration audits.
Assay Video, Melting Curves & Plate Kinetics
Automated curves and figures from DSF melt exports, clearing and fluorescence time-lapses, thermal-camera plates, and 96-well freezing runs.