Hit-finding, docking, co-folding, MD, and FEP — the open-source CADD stack (GROMACS, OpenFE, Boltz-2, OpenFold3) run as one managed Slurm cluster inside your own AWS account. One queue, the right GPU on spot, your data never leaving your VPC. Not a pip install — a cluster operated for you.
3 design-partner slots · BYOC plans from $99/mo · free 30-day pilot
Docking, co-folding, and MM-GBSA rank fast for triage — but still swap rank order within a scaffold, enough noise to advance the wrong compound and burn $400K–1.5M finding out. For the lead-opt call, FEP tracks experiment to 0.38 kcal/mol on the TYK2 benchmark. The hard part was never the algorithm — it was the cluster.
sbatch to ranked hits — watch a full campaign.A 1,000-compound hit-discovery funnel — structure → dock → co-fold → MD, end-to-end in your AWS. One command. 73 minutes. $1.16.
sbatch, unedited wall-clock.
The open-source CADD stack your comp chem team already cites
A managed Slurm cluster in your AWS, the full CADD suite operated end-to-end, and every campaign's ΔΔG history accreting as your program's computational book-of-record.
Perturbation networks, ΔΔG history, MBAR bundles, and per-job cost stamps accumulate in your own EFS — a cost-stamped record that lives in your account, not ours, and compounds into a system no competitor can pull out of your VPC.
Structure prediction (OpenFold3), docking (Uni-Dock, AutoDock-GPU, GNINA), affinity rescoring (Boltz-2), MD (GROMACS, AMBER), and RBFE campaigns (OpenFE, FEP multidir) — the same job queue, Karpenter picks the hardware. No partition routing in your scripts.
Pre-IND structure data is program IP. It stays in your IAM perimeter — not on our infra, not routed through our control plane. BYOC means you see every dollar on your AWS bill, and your Savings Plans apply.
Submit from the web console if you'd rather not touch Slurm. SSH in and sbatch if you live in the terminal. Wire the REST API into your orchestrator if you automate everything.
Browse the CADD template catalog, fill the campaign form, hit submit. Live logs, per-job cost stamp, run history, ΔΔG records. For scientists who'd rather not write sbatch.
sbatch fep-campaign --network edges.csvSlurm-native. SSH in and submit the way you would on any HPC system — same sbatch, squeue, sacct, scancel. For comp chemists who already live in the terminal.
POST /v1/jobs/submitWire Clusterra into your in-house pipeline, Airflow DAG, or Slack bot. JSON in, JSON out. For platform teams that want Clusterra as the compute backend, not the front door.
The same managed Slurm cluster runs all three verticals. Start with the pain that's blocking you now and expand as your program grows.
For the lone comp chemist at a Series A/B small-molecule biotech. OpenFold3 + Uni-Dock + Boltz-2 + GROMACS hit funnel in 73 min at $1.16. RBFE campaigns on the same cluster — no partition routing, no HPC hire.
For structural-biology biotechs running RELION-5 / AreTomo / Warp·M / IsoNet / MemBrain pipelines. Multi-TB tilt-series stay in your VPC. CryoCloud covers SPA — we cover STA. No academic-cluster waitlist.
If you're running nf-core/sarek, AlphaDIA cohorts, MAPPs, single-cell, or a custom Slurm pipeline — the platform substrate is the same. New workloads onboard in days. Send us what you're running.
Not a log file. A tarball any reviewer can rerun end-to-end — with ΔΔG history, MBAR bundles, and per-job cost stamps accreting in your own EFS.
campaign_provenance.tar.gz ├── manifest.json # run metadata + hashes ├── perturbation_network.json # Lomap edge list ├── ddg_estimates.csv # per-edge ΔΔG + MBAR ├── slurm.sbatch # exact submit script ├── container.sha256 # image digest ├── input/ │ └── ligands.sdf / protein.pdb ├── output/ │ └── ranked_hits.tsv / ddg.csv ├── cost.json # per-job AWS cost stamp └── provenance.log # signed, append-only
{ "run_id": "clst-21047", "git_sha": "a3f9e21", "workflow": "fep-campaign@0.3.0", "container": "sha256:4c8a…d9f2", "submitted_at": "2026-06-01T09:14:22Z", "edges": 24, "wall_clock_s": 18420, "cost_usd": 11.40, "nodes": "g5.12xlarge × 1", "protocol_hash": "b91c…d47e", "signed_by": "clusterra-prod" }
Finance can expense it. A new scientist joining next year can clusterra rerun a 2026 campaign and get the same ΔΔG estimates. The SAR history your program accumulates becomes the switching cost that makes the cluster worth keeping.
Spot pricing, checkpoint-restart on, us-east-1. Reproducible benchmarks on public datasets — fork the repo, verify the numbers.
n=1 run verified June 2026, job 2958, TYK2. Spot evictions mid-run; checkpoint-resume recovered every leg with zero lost work. n=3 is required for per-ligand ΔG estimates and error bars — that’s the number we quote. Every dollar lands on your AWS bill, not ours.
Every named competitor has a hard constraint that excludes them from the lone CADD scientist at a Series A/B biotech. Here is the honest map.
| Capability | Clusterra | Rowan | Schrödinger | BioTeam | AWS PCS |
|---|---|---|---|---|---|
| Full CADD suite: hit-find → FEP — operated end-to-end | ✓ | hit-find + docking, no BYOC FEP | FEP+ only with Maestro license | consulting, not SaaS | substrate — you build it |
| Open tools (GROMACS / OpenFE — no proprietary force fields) | ✓ | proprietary TMD engine | OPLS3e, Maestro | ✓ | ✓ |
| BYOC — compute and data in customer’s own AWS | ✓ | VPC tier is bespoke enterprise | virtual cluster, enterprise contract | — | ✓ |
| Simple plan price (no per-seat, no compute markup) | BYOC plans $99–$1,499/mo — you pay AWS for compute, no markup | $200 solo / $50K org / $25 per-cpd | ~$100K+ / year | project billing | per-hr mgmt fee |
| One queue — any job gets the right hardware, no partition routing | ✓ | — | — | — | 10-partition cap, no cross-family |
| Campaign system-of-record (ΔΔG + cost history in your EFS) | ✓ | results on Rowan infra | Maestro project files | — | — |
Rowan wins where the browser UX matters and budget is tight at the per-seat level — it’s a great product for early exploration. Schrödinger wins where the Maestro + OPLS3e stack is already licensed. BioTeam wins where you need custom consulting. AWS PCS is the substrate we’re built on. Clusterra wins when you want the open-source CADD suite operated in your own AWS account at a price a Series A biotech can actually afford — BYOC plans from $99/mo, with compute billed directly by AWS at no markup.
Three steps. All in your AWS account.
BYOC via a cross-account IAM role. Your VPC, your billing, your data. We deploy the Slurm + Karpenter control plane into your account — nothing routes through ours.
Hit-discovery funnel, RBFE campaign, GROMACS FEP multidir, AMBER REMD, OpenFold3 batch — or submit your own Slurm job. The cluster knows what hardware each step needs; you never write a partition name.
sbatch, REST, or the console. Karpenter provisions the right instance family on Spot. Checkpoint-restart on eviction. Live cost meter. Per-job cost stamp. Campaign provenance bundle on every run.
Batch, PCS, and ParallelCluster are those parts pre-sorted but still un-assembled. We deliver the cluster already built, validated, and running — in your own account.
Batch, PCS, and ParallelCluster are kits: someone still has to design the cluster, build the containers, wire up Slurm, and tune the GPUs before a single job runs correctly. That’s a dedicated headcount’s worth of HPC/DevOps work. We hand it to you already built and validated — a managed Slurm cluster running right the day we turn it on.
Spot GPU is ~60–70% cheaper than on-demand, but on raw AWS a long-running job dies the instant the instance is reclaimed — so most teams never use it. We catch the 2-minute reclaim warning, drain the job cleanly, and resume it. The cheap compute becomes usable for the long jobs that actually need it.
On raw AWS you get one monthly bill and no record of how a result was produced. We stamp every job with its dollar cost as it runs — spend visible per experiment, per user, per project — and capture the exact pinned container digest and script behind each run, so any result can be reproduced or re-run months later without rebuilding the environment.
All of that — the day-one cluster, survivable spot, and costed, reproducible runs — for less than a tenth of the hire it would take to build it yourself:
Every plan is the full platform. Plans differ only by how much management credit is included.
For one scientist getting started. Run real campaigns on a proper GPU cluster without committing to anything bigger.
For a team running every week. Pay $499, get $999 of management credit — about 2× the value.
For running hard, with zero math. One flat price covers everything you run — it never changes.
Against any of those, a $99–$1,499/mo management fee is a rounding error — and not a license, a CRO, or a headcount you'd otherwise carry.
For running your cluster — the managed software, the validated scientific stack, spot survival, and provenance. That is the only thing you pay us. The compute itself (GPUs, CPUs, storage) is billed separately and directly by AWS in your own account, at AWS prices — we never touch or mark up that bill.
One scientist, light or occasional runs → Solo ($99/mo, includes $99 of management credit). Running most weeks → Team, the best value ($499/mo, includes $999 of credit — ~2×). Running hard and want one predictable bill → Org ($1,499/mo flat, unlimited, no metering).
“Management credit” is prepaid Clusterra fee — not compute, and not your AWS credits. Solo and Team meter it at one uniform rate, $0.40/GPU-hr + $0.04/vCPU-hr; once the credit is used up you keep paying that same rate, nothing changes. Hours vary by instance; AWS bills the compute separately and directly, at AWS prices.
Yes — this is a real advantage of BYOC. Because compute runs in your own account, your AWS Activate and NVIDIA Inception credits pay for it directly. A SaaS platform that bills you cannot apply those credits — they'd expire unused. Many teams run for months on credits alone; the management fee is the only thing you pay us.
A free 30-day pilot: we stand up your cluster in your AWS, wire your workflows, and get a real campaign running with you — no charge.
Yes — no lock-in. Cancel anytime and changes take effect on your next cycle. Because everything runs in your own AWS account, your data and clusters stay with you.
Or book a free pilot — we get a real campaign running, no charge.
30 minutes to scope. Free 30-day pilot with your first RBFE campaign running in your AWS account — no charge. Then BYOC plans from $99/mo. Three design-partner slots — closes when filled.
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