Fixed-fee sequence, structure, and assay workflows.
Nine computational workflows organized across four R&D suites. Every engagement is scoped in writing at a fixed USD fee under mutual NDA, executed on isolated local hardware by default, and delivered with 100% client IP ownership.
Scoped in writing from $750 to $18,000; never billed hourly
2–10 d
Turnaround
48-hour expedited slots available on Workflows 02, 04, and 07
100%
Client-Owned IP
Zero royalties, zero milestones, and zero sequence ingestion
−15%
Academic Rate
Auto-applied with Net-30 terms for university & institute labs
Four R&D Suites
Select a suite for full protocols, or configure any workflow directly.
Each suite groups adjacent computational steps in the protein engineering and IP lifecycle. Open a suite page for input specifications, deliverables, and tier tables, or jump straight to the scope configurator below.
Filter unstable AI-designed or database candidates before ordering genes, and scrub host-expression liabilities while locking catalytic geometry.
01Pre-Synthesis Stability Screen
300 K & 330 K explicit-solvent OpenMM MD plus disulfide, glycan-shield, and boundary checks on 20–50 candidates—scored against intact and destabilized control structures rather than arbitrary RMSD cutoffs.
Pre-registered control benchmark (1.36 Å separation at 330 K)
Across 10 intact crystal structures vs. destabilized fragment controls at 330 K, 10/10 intact folds held at 1.13 Å mean backbone drift vs. 2.49 Å for controls (1.36 Å separation). Calibrated to filter unstable folds—not to rank active natural homologs.
Active-site-locked redesign generating 10–25 refolded and MD-verified variants free of unpaired ER cysteines, N-glycan traps, protease clips, and oxidation motifs.
Clear Twist, IDT, and GenScript repeat rejections on tandem proteins, rebuild truncated database genes from raw reads, and verify integrated production clones on long reads.
02Repetitive Gene Design & Synthesis Rescue
Synonymous DNA redesign preserving 100% protein identity while clearing vendor repeat/GC screens. No deposit is due on signature; the $4,000 rescue fee is billed only after your vendor’s order-intake screen accepts the construct ($750 pre-check credited in full).
Nanopore and PacBio HiFi single-molecule verification of integration locus, copy number, off-target host disruption, and repeat-array length across 1–12 clones.
Turn raw plate videos, microscope stacks, thermal-camera recordings, and DSF melt exports into clean reaction rates, melting temperatures, and publication figures—without writing custom scripts.
04Assay Video, Melting Curves & Plate Kinetics
Automated calibration and curve fitting across DSF melting curves, polymer and cell-lysis clearing videos, microscope time-lapses, thermal-camera reaction plates, and 96-well droplet freezing runs.
Validated on 27 public benchmark datasets (41,800 frames & 6,964 melt curves)
Covers plate-reader and droplet melting curves (DSF, dMCA, cellular RT-CETSA), clearing and fluorescence stacks (BHET, polyurethane, Exeter Multiscope at r = 0.9405), infrared reaction heat on 96-well plates and microfluidic chips, and frost-corrected droplet freezing.
Source low-identity structural homologs and ancestral nodes, verify genus claim math and WIPO ST.26 XML before filing, or mine SPPS-ready miniproteins.
06Patent-Clear Homolog Search & Ancestral Design
3D structural search, unmasked repeat alignment, and maximum-likelihood ancestral reconstruction delivering diversity-compressed <25%-ID synthesis panels.
Pre-filing mathematical verification of percent-identity and motif genus claims, public sequence/3D collision tables, numbering offsets, and WIPO ST.26 XML compliance.
Discovery and engineering of compact 8–110 residue bioactive peptides, 6-Cys knottin loop grafts, and self-assembling peptide oligomers sized for chemical synthesis or single-AAV vectors.
Single-PO options for recurring assay runs, filings, and R&D queues.
Eliminate per-run procurement cycles with monthly or grant-year assay passes, pre-filing counsel packs, or a reserved workstation queue.
DB-PASS-04-MONTHLY · Workflow 04$1,800 / mo
Daybreak Lab Pass (Monthly or Annual Grant Pass)
Up to 4 assay videos or microscope stacks—or 8 plate-reader exports—per month with 2–3 business day turnaround. Annual Grant Pass available at $12,000/yr (up to 36 runs). Eligible for the 15% academic rate.
Four single-filing technical sequence and claim audits (≤50 SEQ ID NOs each, $3,500 effective per docket vs. $4,500–$6,000 standalone) with 48-hour priority queue access and 12-month validity across client matters.
Onboard DarkBiome once under a single PO or budget transfer and draw down $17,500 in fixed-fee catalog credit across any combination of Workflows 01–09 over 12 months, with itemized balance statements per run.
Reserves one active rolling job slot (up to 45 isolated local GPU-hours/month) across Stability Screening, Synthesis Rescue, Clone Audits, Assay Analysis, Gene Rescue, and Liability Scrubbing. Cancel anytime before renewal.
Clean IP, isolated compute, and explicit technical boundaries.
Built for biotech R&D teams, university PIs, and patent counsel who need reproducible computational deliverables without licensing entanglement.
100% client IP & zero corpus ingestion
You retain full title to all input sequences and project deliverables upon payment, with zero royalties, reach-through claims, or co-authorship requirements. Client sequences never enter DarkBiome’s internal discovery database.
Isolated local execution by default
Proprietary sequences are processed on encrypted local workstations with zero third-party cloud uploads unless you explicitly opt into cloud GPU acceleration in writing.
Written fixed fees & flexible procurement
Every engagement begins with a 1-page written scope. Pay via 50% kickoff deposit, single-transaction university/corporate P-card, or itemized Net-15 / Net-30 Stripe PDF invoice (ACH, wire, or card).
Decision-support & export screening
Deliverables are Research-Use-Only computational analyses and do not replace wet-lab validation or legal opinions from registered patent counsel. Orders undergo standard biosecurity and sanctions screening.
Frequently Asked Questions
Procurement & scope details.
Do I send proprietary sequences in the initial form?
No. Describe only the construct class, approximate batch size, host or assay format, and target timeline. We execute a mutual NDA (yours or ours) before any sequence, structure, or raw sequencing read is transferred.
Can you screen AlphaFold 3, Boltz-2, RFdiffusion, or ProteinMPNN outputs?
Yes. Send FASTA sequences or 3D PDB/mmCIF models across monomers, symmetric or hetero-oligomers, metalloproteins, and giant repeat proteins (up to 2,500 residues in a single pass on our 48 GB workstation, 5,000+ residues via phase-matched window stitching—tested to 8,600 aa—or larger complexes on burst cloud GPUs). We audit boundaries, structural disulfides vs. unpaired ER thiols, and active-site geometry prior to 300 K and 330 K explicit-water OpenMM runs.
How does the $0-if-rejected guarantee on Workflow 02 work?
Under Workflow 02 ($4,000/construct), no deposit is collected at kickoff. We invoice only once your chosen synthesis vendor’s automated order-intake screen accepts the redesigned DNA sequence (preserving 100% amino-acid identity). An optional $750 2-day pre-check is credited 100% toward the redesign.
How does the 15% academic and non-profit rate apply?
Entering a verified university (.edu or international academic institution) or non-profit research institute email in the configurator automatically applies the 15% academic rate and Net-30 invoice eligibility, or allows single-transaction P-card checkout.
What happens if an expedited 48-hour turnaround is missed?
Expedited 48-hour slots (+35% on Workflows 02, 04, and 07 when queue capacity is confirmed at kickoff) automatically revert to the standard base fee if delivery ever slips past 48 hours from data receipt.
Scope & Quote Configurator
Request a 1-page written scope or lock a queue slot.
Select a workflow to preview fixed-fee tiers, turnaround, and deliverables. Request a free 1-page written scope within two business days, or proceed directly to Stripe Checkout or an itemized Net-15 / Net-30 PDF invoice in one step.
