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Release Notes

PROTAC Builder Release Notes

Version 1 organizes PROTAC Builder into a connected educational, component-discovery, assembly, API, and downstream-modeling resource for targeted protein degradation workflows.

The emphasis in this first public release is clarity and workflow fit. The builder remains the central assembly surface, while the surrounding pages explain PROTAC fundamentals, component selection, ecosystem handoff, and responsible interpretation of candidate structures.

Version 1 Released June 9, 2026 Educational and workflow release Validation still required
Launch PROTAC Builder View examples Read how to build a PROTAC Contact the project team

Version 1

Released June 9, 2026. This release turns PROTAC Builder into a more complete public resource for component discovery, degrader assembly, API-oriented workflows, downstream modeling handoff, and project-level documentation.

Version 1 highlights

Educational pages

Expanded primer pages now cover PROTAC fundamentals, component roles, linker design, recruiter selection, and workflow interpretation.

Component hubs

Warheads, linkers, E3 recruiters, and component ecosystem pages now guide users through upstream decisions before assembly.

Connected discovery tools

Warhead Hunter, E3 Ligandalyzer, and V-LiSEMOD are integrated into the site narrative as upstream discovery and inspection tools.

Modeling guidance

Constraint-driven design, in silico modeling, downstream modeling, and benchmarking pages now frame handoff and validation more clearly.

Functional examples

The examples surface now includes direct builder-launch patterns where implemented, including ligand, ligase, and custom SMILES entry points.

Developer resources

API Builder, API docs, OpenAPI schema files, route discovery assets, and batch-oriented resources are now easier to find from the public site.

What changed

Builder and examples

  • The interactive builder remains the main assembly surface for warheads, linkers, and recruiters.
  • The examples page now points users into more functional launch patterns where supported.
  • Implemented launch routes include /builder?ligand=DR7, /builder?ligase=CRBN_Y70, /builder?ligase=VHL_3JS, and /builder?smiles=CCCCC.
Open examples Open builder

Discovery pages

  • Warhead Discovery now connects directly to Warhead Hunter workflows and screenshots.
  • Linker Design now explains bridgeability, rigid and flexible choices, and practical linker cautions.
  • E3 Recruiter Discovery now connects to E3 Ligandalyzer for recruiter-side context.
  • Component Hubs now maps the three core PROTAC component classes together.
Explore component hubs Warheads Linkers E3 recruiters

Resources and developer routes

  • FAQ, Methods, Case Studies, Submit Data, and Release Notes now provide fuller public-facing documentation.
  • API Builder, API docs, batch workflows, OpenAPI JSON, OpenAPI YAML, llms.txt, sitemap, and robots resources are now easier to discover.
  • Database Schema and Download Manifest pages help clarify public route and data surfaces.
FAQ Methods API docs Download manifest

Discovery and ecosystem integrations

External Tool

Warhead Hunter

Supports target-binding warhead discovery, protein-bound ligand inspection, and solvent-exposure review before assembly.

Open Warhead Hunter ↗
External Tool

E3 Ligandalyzer

Supports recruiter, scaffold, and ligase-side structural context before a recruiter is paired in the builder.

Open E3 Ligandalyzer ↗
External Tool

V-LiSEMOD

Supports viral protein-ligand inspection and solvent-exposed moiety review for viral-target warhead workflows.

Open V-LiSEMOD ↗
Core Tool

PROTAC Builder

Remains the assembly and workflow handoff layer where selected components become candidate degrader setups.

Launch builder

Known limitations

Version 1 does not guarantee degradation outcomes.
Builder outputs are candidate hypotheses, not biological proof.
The site is not a complete universal library of all warheads, linkers, or recruiters.
Some workflows depend on upstream data quality and user-provided structures or SMILES.
Computational modeling and experimental validation remain necessary.
API and batch behavior should be checked against the current docs and schemas.
Dataset and feature availability may change as the public site evolves.

What is next

Planned or candidate directions may change as the project evolves, but near-term priorities include more detailed case studies, richer builder launch examples, clearer downloadable workflow checklists, expanded API and batch guidance, more cross-tool handoff examples, and better benchmark-ready metadata capture.

Examples

More end-to-end example workflows can make it easier to translate abstract concepts into reproducible builder setups.

Documentation

API, batch, and workflow reporting guidance can become more explicit as users contribute feedback.

Handoffs

Cross-tool examples and downstream metadata conventions can continue to improve the quality of structural handoff.

Feedback

Found a broken link, unclear workflow, or missing example? Help us improve Version 1 by sending structured feedback, contribution ideas, or ecosystem update requests.
Submit feedback Open GitHub ↗ Contact the project team