A thousand seeds.One binder.
Senbazuru — fold a thousand, grant one wish.
Twelve protein-design tools, one workflow. Point at a target, route across RFdiffusion, BindCraft, Boltz-2 and the rest, and rank survivors under a single rubric.
Designing a binder shouldn’t feel like gambling.
Every tool claims SOTA. None of them agree.
ProteinMPNN wins on one target, RFdiffusion on the next, BindCraft on a third. There's a right tool for your target — but nobody's measured which.
A thousand seeds is a weekend of shell scripts.
Conda conflicts. CUDA mismatches. Silent failures at seed 847. You came to design proteins, not maintain containers.
Every benchmark is a different ruler.
Each tool reports on its own target with its own scoring. We run every major tool against the same three targets, with one rubric and pre-registered thresholds — and publish the full dataset.
Four folds, then a crane takes shape.
From PDB to ranked candidates in a single run — no Conda, no orphaned shell scripts, no silent failures at seed 847.
Upload your target.
Drop a PDB, specify a hotspot — or let us infer one. We parse topology, surface, and interface class in under a second.
We allocate the seeds.
Our routing algorithm reads your target — helical bundle, β-sheet, disordered loop — and distributes budget across the tools most likely to bind your geometry.
Everything runs in parallel.
BYO compute on Free. Managed GPUs on Pro. Dedicated cluster on Frontier. No Conda. No CUDA. No seed 847.
Ranked candidates, order-ready.
Every design scored by ipSAE, DockQ, pTMEnergy. Download the top 10, export to Twist, or push straight to a wet-lab partner.
Every tool, version-pinned, containerized, benchmarked.
A curated index of every protein design tool worth running — with reproducible environments, pinned weights, and head-to-head metrics on the same targets.
RFdiffusion
ProteinMPNN
BindCraft
Chai-1
Boltz-2
Chroma
LigandMPNN
AlphaFold 3
We publish the methodology before the results.
Targets, hotspots, seed counts, hit thresholds, and statistics are declared up front in a signed, versioned specification, so no threshold can be chosen after the fact.
Runs are not published yet. The leaderboard opens when a run set reproduces from a clean environment against those pre-registered criteria — not before.
The protocol is public and frozen. The runs are not published yet — the execution pipeline is still being validated end-to-end, and we will not show a number we cannot reproduce from a clean environment. The leaderboard appears here the day the first run set clears that gate, against thresholds that were written down long before we saw them.
- Pre-registered
- Targets, hotspots, seed counts, hit thresholds, and statistics were fixed and published before any run was scored. Nothing can be tuned after seeing results.
- Signed & versioned
- Methodology v1.0 is git-signed and immutable after publication. Changing a threshold, target, or statistic forks a new version with a public diff.
- External advisory panel
- Three external members — structural biology, experimental protein engineering, and ML methodology — review methodology changes and adjudicate reproducibility disputes.
- 7-day public comment
- Every proposed new target goes through a seven-day public comment window before the panel votes on admission.
Three folds. No surprises.
Free tier is free, forever. Pro is a flat subscription plus metered compute. Frontier is annual, invoiced, with a named account lead. That’s it.
- Every open-source tool
- Bring your own compute
- Public leaderboard access
- Community support
- 7-day data retention
- Managed GPU, metered
- 50,000 seeds / month
- Private campaigns
- Priority queue
- Email support · 24h
- 90-day retention
- Closed frontier models
- Dedicated cluster
- VPC or on-prem deploy
- Custom tool integration
- Shared Slack · 1h SLA
- SOC 2 · HIPAA eligible
Two high-schoolers who got tired of Conda.
We’re Harsha Poonepalle and Vedant Kalipatnapu — iGEM co-captains and international winners at the iGEM Grand Jamboree. We spent a full season running ProteinMPNN, RFdiffusion, and BindCraft against the same target, by hand, one seed at a time. We lost three weekends to environment conflicts before we shipped a single design that worked.
We built Paper Crane because we wanted the tool we couldn’t find. Advised by Dr. Bryan Bryson (MIT Biological Engineering), Dr. Metzker (ex-MIT/Harvard, bio founder), plus faculty at UCLA and UPenn. Our early users include iGEM teams across four continents.
We believe the next generation of therapeutics will be designed, not discovered — and that the platform underneath should be as elegant as the proteins it builds.
The answers to the questions.
Free is free forever on your own hardware. Pro is a flat monthly subscription plus metered compute (pennies per seed). Frontier is annual, invoiced, with a dedicated account manager.
Every major open-source tool: ProteinMPNN, RFdiffusion, BindCraft, Chroma, Genie2, LigandMPNN, ESM-IF, BoltzDesign, plus validators (AF3, Boltz-2, Protenix, Chai-1). Closed partners available on Frontier.
Yes. On Pro, your inputs and outputs are encrypted at rest and never used for training. On Frontier we deploy into your VPC — we never see your data. Free tier runs on your own hardware, so privacy is yours.
Yes. Open a PR on our catalog repo with a Dockerfile and a benchmark run. We review weekly. Frontier customers get white-glove integration of proprietary tools.
Pro and Frontier are SOC 2 Type II (in progress) and HIPAA-eligible. All traffic TLS 1.3, storage AES-256, compute in sandboxed containers. Frontier deploys within your cloud account.
No. Your designs are yours. We don't own them, license them, or patent them. We're a platform, not a partner on your IP.
A thousand seeds. One binder.
Start folding.
Join the iGEM teams, academic labs, and biotechs already on the waitlist. No credit card. Free forever on your hardware.