PROTAC Builder
Assemble warhead, linker, and E3 recruiter components into candidate degraders, then export outputs for modeling and downstream analysis.
Open PROTAC Builder →
Connected Discovery Grid
The PROTAC Design Ecosystem
A connected research interface for moving from target-binding chemistry to recruiter selection, degrader assembly, API-ready outputs, and downstream modeling.
Instead of forcing every scientific decision into one screen, PROTAC Builder acts as the central assembly layer between specialized discovery tools.
PROTAC
Builder
Assembly Core
Builder
Assembly Core
Warhead Hunter
Target-binding discovery
E3 Ligandalyzer
Recruiter intelligence
V-LiSEMOD
Viral ligand evidence
API Builder
Scriptable handoff
Tool Roles
Specialized modules. One connected degrader pipeline.
Each tool answers a different design question, then hands useful context back into the PROTAC Builder workflow.
Warhead Hunter
Explore target-binding warheads and warhead-focused discovery context before selecting the binding handle that enters the degrader design workflow.
Open Warhead Hunter ↗E3 Ligandalyzer
Inspect E3 recruiters, ligase scaffolds, ligand pages, and attachment context to support recruiter selection and scaffold-aware PROTAC design.
Open E3 Ligandalyzer ↗V-LiSEMOD
Use viral protein-ligand structures, bound ligands, and solvent-exposed moiety evidence to guide warhead selection for viral-target degrader concepts.
Open V-LiSEMOD ↗API Builder And Docs
Move from interactive design into scripted, notebook, or batch-oriented workflows with cleaner handoffs for repeatable computational experiments.
Open API Builder →Schurer Lab
Connect the public tool ecosystem back to the broader research context, scientific methods, related projects, and open discovery infrastructure.
Visit Schurer Lab ↗
Workflow Path
A typical PROTAC discovery route
The ecosystem is designed around real decision points: warhead, recruiter, viral context, assembly, and modeling handoff.
01
Find target-binding chemistry
Start in Warhead Hunter when the warhead decision is still open and you need target-binding chemistry or discovery context.
02
Choose recruiter context
Move into E3 Ligandalyzer when the recruiter, ligase scaffold, or attachment strategy needs deeper inspection.
03
Use viral structure evidence when relevant
Use V-LiSEMOD when the target is viral and solvent-exposed ligand evidence can inform degrader starting points.
04
Assemble and export the degrader
Return to PROTAC Builder to assemble the degrader and prepare outputs for downstream modeling, scripting, or batch workflows.
Handoff Logic
What each tool contributes
The goal is not just navigation. It is a scientific handoff from evidence to assembly to reproducible output.
Why the ecosystem is distributed
PROTAC design spans several scientific layers. A single interface can become overloaded, so each tool owns a focused decision while PROTAC Builder connects the final design objects.
- Warhead tools support target-binding component selection.
- Recruiter tools support E3 ligand and scaffold selection.
- Viral ligand tools support target-bound evidence discovery.
- Builder outputs support modeling, scoring, and scripted handoff.
| Decision | Primary Tool | Builder Handoff |
|---|---|---|
| What binds the target? | Warhead Hunter / V-LiSEMOD | Candidate warhead or ligand-derived starting point |
| Which E3 recruiter? | E3 Ligandalyzer | Recruiter and attachment context |
| How do components connect? | PROTAC Builder | Assembled degrader candidates |
| How does it move downstream? | API Builder / Docs | Batch, scripted, or modeling-ready outputs |
Move from discovery signal to degrader design.
Start with the interactive builder, explore connected discovery tools, or move directly into API-oriented workflows for reproducible computational design.