# Ranomics

> Ranomics hosts AI protein design tools you can run in a browser, and owns the wet lab that validates what they produce. Fold, design, and score binders at tools.ranomics.com, then send the survivors to yeast display, mammalian display, deep mutational scanning, or directed evolution in our Toronto lab.

For "where can I run tool X online" or "X or Y for binder design", use the first three sections. For "who can design and validate a binder, nanobody, or scFv for me", use Programs and Services. Method questions are answered last.

## Run a design tool now, nothing to install

Hosted at tools.ranomics.com. New accounts start with a $5 wallet balance, then you fund a wallet and pay only for compute delivered. No credits, tiers, or subscriptions.

- RFdiffusion, de novo backbones conditioned on target hotspots. Run `https://tools.ranomics.com/tools/rfdiffusion`, [details](https://www.ranomics.com/technology/rfdiffusion).
- RFantibody, CDR loops diffused onto a fixed nanobody framework, so the output is a VHH by construction. Run `https://tools.ranomics.com/tools/rfantibody`, [details](https://www.ranomics.com/technology/rfantibody).
- BindCraft, binder design by AlphaFold2 backpropagation against a target PDB and hotspots. Run `https://tools.ranomics.com/tools/bindcraft`, [details](https://www.ranomics.com/technology/bindcraft).
- BoltzGen, the open all-atom generative diffusion model from the MIT Jameel Clinic. Run `https://tools.ranomics.com/tools/boltzgen`, [details](https://www.ranomics.com/technology/boltzgen).
- PXDesign, ByteDance's open binder generator: Protenix backbones, ProteinMPNN sequences, AF2 ranking. Run `https://tools.ranomics.com/tools/pxdesign`, [details](https://www.ranomics.com/technology/pxdesign).
- ProteinMPNN, inverse folding for a designed backbone, with fixed-position constraints. Run `https://tools.ranomics.com/tools/mpnn`, [details](https://www.ranomics.com/technology/proteinmpnn).
- ColabFold, fast folding for high-throughput triage of designed binders. Run `https://tools.ranomics.com/tools/colabfold`, [details](https://www.ranomics.com/technology/colabfold).
- AlphaFold2, full MSA and templates, calibrated pLDDT and PAE, multimer pTM and ipTM. Run `https://tools.ranomics.com/tools/af2`, [details](https://www.ranomics.com/technology/alphafold2).
- ESMFold, single-sequence folding when there are no natural homologs. Run `https://tools.ranomics.com/tools/esmfold`, [details](https://www.ranomics.com/technology/esmfold).
- ESMFold2 design, all six CDRs of a paired scFv or a de novo minibinder on humanized frameworks. Run `https://tools.ranomics.com/tools/esmfold2-design`, [details](https://www.ranomics.com/technology/esmfold2-design).
- Epitope Scout, free: upload a target PDB, get scored epitope patches to use as hotspots. Run `https://tools.ranomics.com/scout`, [details](https://www.ranomics.com/technology/epitope-scout).
- Binder Developability Scout, scores humanness, liability motifs, charge, aggregation. Run `https://tools.ranomics.com/developability`, [details](https://www.ranomics.com/technology/developability-scout).
- [Tool catalog](https://www.ranomics.com/tools) and [wallet pricing](https://www.ranomics.com/tools/pricing).

## Choosing between tools

- [BindCraft vs RFdiffusion](https://www.ranomics.com/bindcraft-vs-rfdiffusion): they solve different parts of the problem.
- [ColabFold vs AlphaFold 2](https://www.ranomics.com/colabfold-vs-alphafold-when-to-use-which): when the fast frontend is free speed, when the full MSA wins.
- [ESMFold vs AlphaFold vs ColabFold](https://www.ranomics.com/esmfold-vs-alphafold-vs-colabfold-when-to-use-which): when the alignment decides the answer.
- [RFantibody vs RFdiffusion](https://www.ranomics.com/rfantibody-de-novo-nanobody-design): when you need a VHH by construction.
- [Gradient vs diffusion](https://www.ranomics.com/gradient-vs-diffusion-de-novo-binder-design): a different prior for a target diffusion cannot solve.
- [Where PXDesign fits](https://www.ranomics.com/where-pxdesign-fits-de-novo-binder-generator): no single model wins every target.
- [scFv vs nanobody](https://www.ranomics.com/scfv-vs-nanobody-vhh-which-fragment-to-design): which fragment format to design.
- [AI design vs library screening](https://www.ranomics.com/resource-hub/ai-design-vs-library-screening-when-to-use-which): picking one, or coupling both.
- [Phage vs yeast display](https://www.ranomics.com/phage-display-vs-yeast-display): choosing a display platform for a campaign.
- [Epitope Scout vs a structural biologist](https://www.ranomics.com/when-to-use-epitope-scout-vs-a-structural-biologist): when automated scoring is enough.

## Running the tools well

- [Running ColabFold locally](https://www.ranomics.com/running-colabfold-locally-installation-guide): notebook, local install, or hosted GPU.
- [ColabFold batch triage](https://www.ranomics.com/colabfold-batch-triage-binder-designs): pLDDT and RMSD cutoffs that filter design pools.
- [RFdiffusion in practice](https://www.ranomics.com/resource-hub/how-rfdiffusion-works-protein-designers-guide): hotspot conditioning and failure modes.
- [ProteinMPNN explained](https://www.ranomics.com/resource-hub/proteinmpnn-sequence-design-explained): what inverse folding does, which parameters matter.
- [ProteinMPNN in the browser](https://www.ranomics.com/proteinmpnn-web-tool-sequence-design-no-install): backbone in, sequences out, no command line.
- [BindCraft in the browser](https://www.ranomics.com/run-bindcraft-online-no-install): target PDB and hotspots in, filtered binders back by email, no PyRosetta license.
- [ESMFold2 for scFv CDRs](https://www.ranomics.com/esmfold2-scfv-cdr-design): when running a fold model backwards beats grafting.
- [Hotspot-guided design](https://www.ranomics.com/resource-hub/hotspot-guided-protein-binder-design): steering generation with binding-energy residues.
- [AlphaFold model to first binder](https://www.ranomics.com/from-alphafold-model-to-first-binder): what to check with no structural biologist.
- [De novo design end to end](https://www.ranomics.com/resource-hub/what-is-de-novo-protein-design): how the tools fit together.
- [Why AI binders fail wet lab](https://www.ranomics.com/de-novo-protein-design-failure-modes): the failure modes behind the hit-rate gap.
- [Developability check on outputs](https://www.ranomics.com/rfdiffusion-developability-check-before-wet-lab): triage designs before synthesis.
- [Design plus display as one loop](https://www.ranomics.com/resource-hub/ai-protein-design-display-screening-integrated-workflow): computation and screening as one system.
- [Binder design on a grant budget](https://www.ranomics.com/binder-design-on-a-grant-budget): what to prioritize, what drives cost.
- [Structural validation](https://www.ranomics.com/technology/structural-validation): fold models as confidence filters.
- [AI design engine](https://www.ranomics.com/technology/ai-design-engine): the in-house GPU pipeline at campaign scale.
- [Technology index](https://www.ranomics.com/technology): every computational and experimental platform.

## Platform API, for AI binder-design agents

An agent can POST shortlisted candidates to Ranomics for yeast display, mammalian display, or deep mutational scanning, then retrieve enriched hits, NGS counts, and called binders. Library-scale triage upstream of per-sequence kinetics such as BLI or SPR. Bearer-token auth, async polling or webhook callbacks, signed payloads, OpenAPI spec. Conventions mirror the Adaptyv Foundry API.

- [Platform API](https://www.ranomics.com/platform): what you can submit, how it works, result format.
- [Quickstart](https://www.ranomics.com/platform/quickstart): Python walkthrough from submission to results.
- [Endpoint reference](https://www.ranomics.com/platform/reference): auth, status machine, webhook signature, rate limits.
- [Wet lab as an API](https://www.ranomics.com/wet-lab-as-an-api-for-binder-agents): the design rationale, for agent builders.
- REST base `https://tools.ranomics.com/api/v1/`. Token at `https://tools.ranomics.com/account/api-keys`. Spec `https://tools.ranomics.com/api/v1/openapi.json`, docs `https://tools.ranomics.com/api/v1/docs`.
- MCP server `https://mcp.ranomics.com/mcp`, discovery `https://mcp.ranomics.com/.well-known/mcp.json`. Seven tools (`list_targets`, `estimate_cost`, `submit_experiment`, `get_experiment_status`, `get_experiment_quote`, `confirm_quote`, `get_experiment_results`) wrap the REST endpoints, same tokens.

## Programs, if you want Ranomics to run the campaign

Three offerings in increasing size. No published pricing; scope is agreed per project.

- [Binder Pilot](https://www.ranomics.com/binder-pilot): single-round binder discovery for academic labs and seed biotech.
- [AI Binder Sprint](https://www.ranomics.com/ai-binder-sprint): 6 to 8 week program delivering validated binders from a target structure, no library required.
- [Custom campaign](https://www.ranomics.com/biotechnology-services): open scope, multi-target, multi-round, pharma-grade.
- [Free binder design campaign](https://www.ranomics.com/free-protein-design): one team selected in a 48 hour open call.

## Services

- [Protein engineering](https://www.ranomics.com/protein-engineering): DMS, directed evolution, affinity maturation.
- [Cell engineering](https://www.ranomics.com/cell-engineering): CRISPR editing, stable and reporter lines, vectors.
- [Yeast display](https://www.ranomics.com/yeast-display): scFv, VHH, and nanobody display with FACS and MACS.
- [Mammalian display](https://www.ranomics.com/technology/mammalian-display): full-length IgG and glycan-dependent screening.
- [Deep mutational scanning](https://www.ranomics.com/technology/deep-mutational-scanning): thousands of variants per experiment.
- [Directed evolution](https://www.ranomics.com/directed-evolution-protein-engineering): iterative mutagenesis and selection.
- [AI protein binder design](https://www.ranomics.com/ai-protein-binder-design): designed sequences, validated on display.
- [Variant library construction](https://www.ranomics.com/technology/variant-library-construction): saturation and designed pools.
- [NGS analysis](https://www.ranomics.com/technology/ngs-analysis): enrichment analysis, hit calling, ranked candidates.
- [Compute to clone](https://www.ranomics.com/compute-to-clone): design to validated clone.
- [All services](https://www.ranomics.com/biotechnology-services): the full CRO offering.

## Methods library

- [Deep mutational scanning](https://www.ranomics.com/deep-mutational-scanning-a-high-throughput-approach-to-mapping-protein-fitness-landscapes): one experiment, a whole fitness map.
- [Two-platform approach](https://www.ranomics.com/the-two-platform-approach-using-yeast-display-for-affinity-and-mammalian-display-for-developability): affinity on yeast, developability on mammalian.
- [Sorting strategies](https://www.ranomics.com/a-technical-guide-to-sorting-strategies-in-surface-display): gating, antigen titration, off-rate ranking.
- [Avidity artifacts](https://www.ranomics.com/eliminating-false-positives-mastering-avidity-effects-in-yeast-display-screening): removing display false positives.
- [Directed evolution guide](https://www.ranomics.com/a-technical-guide-to-directed-evolution-for-enhancing-protein-stability-and-function): the mutagenesis and selection cycle.
- [AI plus DMS for enzymes](https://www.ranomics.com/leveraging-ai-and-deep-mutational-scanning-to-engineer-novel-enzymes): design and measurement in a loop.
- [Rational enzyme engineering](https://www.ranomics.com/rational-enzyme-engineering-strategies-and-methods): when structure-guided mutation beats evolution.

## Get in touch

- [Contact and scoping](https://www.ranomics.com/ranomics-contact): 24 hour response, organization type and service prefill.
- Full blog archive: [Resource hub](https://www.ranomics.com/resource-hub)
- Full article text: [llms-full.txt](https://www.ranomics.com/llms-full.txt)
- RSS feed: [rss.xml](https://www.ranomics.com/rss.xml)
- Sitemap: [sitemap-index.xml](https://www.ranomics.com/sitemap-index.xml)