Precomputed demo
AlphaGene Protein Design Studio
From target structure to designed protein candidates.
Explore a prepared target-to-design run. This page replays previously computed RFdiffusion and ProteinMPNN outputs; it does not start a live GPU job.
- 01Define targetKv1.3 channel interface
- 02Generate backboneRFdiffusion candidate set
- 03Design sequenceProteinMPNN with fixed motif
- 04Review candidateStructure and method checks
Experimental reference structures
Classic Binding Atlas
See how established ligands and inhibitors engage their targets.
Explore nine landmark binding stories across oncology, metabolism, immunology, and infectious disease. Each view replays a public experimental structure from the Protein Data Bank—not a newly generated AlphaGene result.
Immuno-oncology
PD-1 checkpoint blockade
Compare the natural checkpoint interface with clinically established antibody complexes.
Experimental complex
Drag to rotate · pinch or scroll to zoom · right-drag to move
Loading experimental structure
Reading coordinates from the local case library.
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Structure could not be loaded.
Choose another case or download the PDB for local inspection.
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Three-step explanatory view · not a molecular-dynamics trajectory.
Target
Binding partner
Interface residues
- Method
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- Resolution
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- Displayed chains
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What this structure does—and does not—show
Reference-library boundary
These are public experimental structures used to explain molecular recognition. Static coordinates do not establish affinity, selectivity, efficacy, safety, or real-time binding dynamics. Antibody entries show Fab fragments where indicated; receptor entries may show only experimental domains or ectodomains. View structure provenance.
Interactive workspace
Replay a real prepared binder-design example.
Interactive 3D complex
AG-KV13-001
Stage 04 / 04
Review candidate
Illustrative transition · not RFdiffusion timesteps
Loading prepared structure
Parsing target and binder coordinates in your browser.
Structure could not be loaded.
Refresh the page or download the PDB to inspect it locally.Prepared candidate set
Compare backbone and sequence outputs.
Choose a card to load its complex, sequence, metrics, and downloads.
ProteinMPNN sequence
AG-KV13-001
- Sequence length
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- Backbone Rg
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- ProteinMPNN score
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- Backbone assessment
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Structure-consistency review
Evidence available in this run
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Included
RFdiffusion backbone complexTarget chain B and designed binder chain A
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Included
ProteinMPNN sequence designFixed Lys–Tyr motif and recorded model score
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Not run
Independent fold-back predictionNo AlphaFold, ColabFold, or ESMFold score is claimed
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Not run
Experimental binding validationNo affinity, specificity, safety, or efficacy data
Computational structure-consistency checks do not establish binding affinity, specificity, stability, safety, efficacy, or experimental validation.
Methods and provenance
Every displayed artifact has a traceable role.
Public target system
A 7SSZ-derived Kv1.3 channel/toxin system supplies the prepared target geometry and interface context.
RFdiffusion backbones
Three real outputs from the official RosettaCommons binder-design tutorial form the candidate set.
ProteinMPNN sequences
Sequences were generated for each binder backbone with the tutorial's Lys–Tyr motif held fixed.
Optional live validation
A private GPU backend can add fold-back prediction, complex scoring, queues, and project persistence.
From demo to live platform
Connect a private GPU worker when you are ready to calculate new designs.
The current experience is a zero-GPU-cost prepared demonstration. A live deployment can keep the same interface while adding customer accounts, private uploads, job queues, and project history.
Discuss a private design run