# DarkBiome

> DarkBiome LLC searches public genomes and metagenomes for industrial enzyme candidates, models and simulates them in explicit solvent, and licenses them for evaluation. Out of the dark. Into the reactor. Every result below is computational unless a page says otherwise: structures are predicted models, and activities and operating envelopes are predictions or design targets.

## Scale
- Corpus: a 2.3 TB archive of public sequence — metagenomic reads, assembled genes, isolate genomes and protein catalogs, from sources including EMBL-EBI MGnify, NCBI, JGI and UniProt — holding hundreds of millions of sequence records in 29,000+ files.
- Distinct sequences evaluated: ~400M (novel-insertion counter of deduplication Bloom filter).
- Screened by Tier 1 prefilter: 152.6M (41-head neural classifier on Apple Neural Engine, up to 14,200 sequences/s).
- Folded 3D structure models: nearly 1 million distinct sequences with predicted structures.
- Candidate records in registry: 16,615,827.
- Scored candidates: historical cumulative database record; live re-scoring is scheduled.
- Discovery target programs: 35 active discovery programs across five domains and six structural archetypes (`catalytic_pocket`, `metal_coordination`, `aromatic_network`, `multi_domain_cassette`, `idp_charge_pattern`, `solenoid_lattice`).
- Stage gates: Standardized platform progression gates:
  1. **In Silico Validated**: target identified, structural fold validated, biophysical stability confirmed via molecular dynamics.
  2. **CRO Synthesis Queued**: expression cassettes designed, codon-optimized, and queued for commercial CRO gene synthesis.
  3. **USPTO Patent Filed**: priority patent application filed covering novel composition of matter and functional architectures.
- Biophysical validation & diagnostics:
  - Sub-angstrom catalytic calipers evaluating active-site triad geometries.
  - Metalloenzyme coordination geometry analysis evaluating cofactor binding and active-site pocket assembly.
  - Aromatic percolation network modeling to verify electronic and structural packing.
  - Charge patterning profiles for intrinsically disordered proteins and biomaterials.
  - Independent deep-learning topology verification and strict secretion boundary modeling.
  - All-atom explicit-solvent molecular dynamics (OpenMM 8.0, TIP3P/TIP4P-Ice) at process temperatures (0°C–70°C).
  - Interactive discovery console with instant *E. coli* and *Pichia pastoris* codon optimization export.
- Bench app: DarkBiome Daybreak, macOS and Windows application for automated plate assay analysis (droplet-freezing kinetics, clearance, microcalorimetry, thermal shift).
- Company: DarkBiome LLC, a Delaware limited liability company, headquartered in Alameda, California. Synthesis is outsourced to qualified CROs under bilateral agreements.
- Patents: Priority provisional applications filed with the USPTO covering novel ice-nucleation architectures (applications 64/162,890, 64/165,496, and 64/165,502). Additional specifications queued.

## Lead programs
- [Discovery portfolio](https://darkbiome.bio/pipeline): Filterable table of 35 industrial programs across five domains, with mined counts, folded models, and stage gates.
- [Psychrophilic Arctic marine PETase (DBM-PETase)](https://darkbiome.bio/pipeline/petase): From an Arctic surface-water metagenome. Stage gate: In Silico Validated. Catalytic triad architecture predicted to depolymerize post-consumer PET at 0°C–15°C without steam heating ($6.2B target market).
- [Soluble bacterial C3 INP homotrimer (DBM-INP1)](https://darkbiome.bio/pipeline/inp): From an environmental metagenome. Stage gate: CRO Synthesis Queued (U.S. provisional application 64/165,496). Soluble 3 × 514 AA homotrimer with three radial ice-binding faces 120° apart and self-capping stalk, lacking insoluble transmembrane anchors ($2.5B–$5.0B target market).
- [Fusarium bilayer ice press (DBM-INP2)](https://darkbiome.bio/pipeline/inp): From *Fusarium avenaceum*. Stage gate: USPTO Patent Filed (U.S. provisional application 64/162,890). β-hairpin sandwich whose 6.5 Å cleft templates a 2D bilayer of hexagonal ice in explicit-solvent simulation ($1.8B target market).

## Licensing framework
- Stage 1, confidential evaluation package: Structured under bilateral Delaware CDA/MTA, 100% credited against definitive license. Funds custom synthesis of 50 mg to 250 mg of purified enzyme at a qualified CRO for blinded partner validation. DarkBiome holds no physical stock.
- Stage 2, definitive commercial license: Worldwide field-exclusive rights; $500,000–$750,000 upfront technology transfer; $1,250,000–$2,000,000 development milestones; 4.0%–5.0% running royalties; 20% NRSI.

## Diligence and contact
- Diligence, CDA, dataroom and evaluation requests: DarkBiome Licensing Team <licensing@darkbiome.bio>
- General contact: <info@darkbiome.bio>
- Website: https://darkbiome.bio
- Full technical reference: https://darkbiome.bio/llms-full.txt
- Discovery engine: https://darkbiome.bio/technology
- Discovery portfolio: https://darkbiome.bio/pipeline
- Licensing terms: https://darkbiome.bio/licensing
- Company: https://darkbiome.bio/about
- Contact form: https://darkbiome.bio/contact
- Privacy notice: https://darkbiome.bio/privacy
- Terms of use: https://darkbiome.bio/terms