SynthyraThe Platform
The interactome,
answerable in seconds.
Synthyra builds protein language models that screen any protein or molecule against the entire proteome: 375 million interactions per second, across species. Proteome-scale interaction mapping and protein design for medical research and biosecurity.
The Problem
We grasp the parts. The connections are what's missing.
The human proteome contains over 20,000 proteins and more than 400 million possible pairwise interactions. Existing databases catalog only a fraction of them. The rest are untested, unpublished, unknown. Synthyra screens the relevant interaction space for each query and returns a ranked hypothesis map: predicted partners, functional annotations, pathway enrichment, and a structure model for follow-up.
0%
of drugs fail clinical trials
0%
because of unmanageable toxicity
$0M+
average cost of late-stage failure
The Engine
Atlas
A chemical language model that predicts protein-protein and protein-ligand interactions at proteome scale. The engine behind every query.
Proteome-Scale
Screen against all 20,000+ human proteins in a single query
Real-Time
375 million interactions per second
Validated
AUROC 0.82 with wet-lab confirmed designs
Atlas in context
Atlas makes biology navigable.
The same model can connect ligands to confident targets, trace nearby protein neighborhoods, and project those signals back into biological features researchers already use.
Explore all demosPLI + PPI
How Atlas connects ligands to pathways.
FDA ligands highlight confident protein targets, then show the PPI neighborhoods likely to be perturbed.
Loading PLI + PPI
Cell maps by SIB Swiss Institute of Bioinformatics, CC BY 4.0
Value
Three pillars. One platform.
Faster Cures
Query any target protein and generate ranked interaction hypotheses, confidence scores, pathway enrichment, and functional annotations for follow-up experiments.
Life Sciences Hypothesis Workflow
Rapid Defense
Screen pathogen proteins against the full human proteome in seconds to protect national security and respond to emerging threats. Predict cross-species interactions across 8+ organisms, including novel host-pathogen pairs no database has cataloged.
Biosecurity Suite
Safer Drugs
Screen drug candidates against the entire proteome to surface off-target interactions. Functional annotations flag solubility, stability, and localization risks before you reach the clinic.
Safety & Toxicity Suite
Solutions
Purpose-built product suites.
Focused maps for teams that need to turn latent biological structure into ranked hypotheses, risk decisions, and actionable response.
Safety & Toxicity
PLI context for off-target risk.
Atlas PLI places FDA-approved ligands and human protein targets on the same map, turning off-target screening into a navigable risk surface before clinic-bound programs harden.
34.1M high-confidence PLI edges across FDA ligand and protein space.
FDA-approved drug neighborhoods
Proteome-wide off-target hypotheses
Protein target context for mechanism and safety narratives
Biosecurity
Inter-actomes for host-pathogen response.
Atlas maps pathogen and human proteomes in one interaction field so teams can triage host-pathogen edges, exposed host systems, and countermeasure routes, turning an emerging threat into a navigable target list in hours, not months.
Cross-species actome views spanning pathogen and human proteins.
Host-pathogen edge prioritization for rapid response
Human target context for countermeasure design
Cross-organism interaction maps built for national-security timelines
Validation
Built on evidence. Verified in the lab.
Independent benchmarks, third-party wet-lab validation, millions of open-source downloads, billions of protein interactions screened.
MCC vs current state-of-the-art
Matthews Correlation Coefficient, Bernett Gold-standard PPI benchmark
Intra-species interactions, consistent across taxonomic diversity
Human, mouse, yeast, D. melanogaster, E. coli, C. elegans, D. rerio, A. thaliana.
Inter-species interactions, first better than random chance on human|sars-cov-2 interactions
human|sars-cov-2, human|sars-cov, human|hpv, human|hiv, human|hhv, human|mouse, human|rat, human|yeast, BIOGRID
0
AUROC: Core PPI prediction
Internal held-out evaluation sets, homology-aware clustering (30%), C3 dataset split by cluster
0
Novel predicted interactions characterized, 80 more on the way
BLI validation, Adaptyv Bio (third-party)
Model downloads
First version was open-source, global researcher adoption
Binding visualization
EGFR Binder Case Study
Wet-Lab ConfirmedSynthyra designed a variant of cetuximab (in orange), a multi-billion dollar cancer therapeutic, with 87% stronger binding affinity (630 pM Kd) to EGFR (in green). 13 designs tested, 11 strong binders, 1 medium binder, 5 sub 3 nM Kd, 6 stronger than cetuximab.
Biolayer Interferometry on recombinant targets, SDS-PAGE QC. Adaptyv Bio
STRING vs. Atlas
From known interactions to ranked hypotheses.
STRING is the gold standard for known protein interactions. Atlas turns the unknown space around proteins and small molecules into hypotheses teams can test.
STRING
- Excellent for exploring established biology
- Catalogs interactions from literature, experiments, databases, and computational evidence
- Coverage follows available evidence and periodic database updates
- Does not generate proteome-scale PPI and PLI hypotheses from a single query
Atlas
- Generates ranked PPI and PLI hypotheses at proteome scale
- Surfaces interaction networks for untested proteins and small molecules
- Adds functional annotations, pathway enrichment, and structure models for follow-up
- Supports life-sciences workflows across safety, toxicity, and biodefense
STRING tells you what's known. Atlas helps generate what to test next.
The Destination
Beyond discovery, engineering biology itself.
The same platform that protects national security and accelerates medical research today is the foundation for our longer-term destination: metabolic engineering. We're designing biological systems to replace petrochemical processes, a powerful, green alternative to traditional synthetic chemistry.
Climate change
Engineer biological routes to fuels, materials, and chemicals that displace carbon-intensive petrochemistry.
Resource depletion
Build renewable, biology-driven manufacturing that breaks dependence on finite fossil feedstocks.
Human health
Turn proteome-scale understanding into the design of systems that confront disease at its source.
The interactome, answerable in seconds.
Request access to Discover and turn a protein or small molecule into a ranked life-sciences hypothesis map before the next experiment is designed.
or reach out at [email protected]