PROTAC Builder is a component assembly and workflow handoff tool. It helps users turn warheads, linkers, and E3 recruiters into candidate degrader structures while keeping component boundaries, attachment atoms, and downstream-ready representations explicit.
The builder is not framed as a complete biological prediction engine. It supports disciplined candidate preparation so downstream modeling, reporting, and experimental planning can be more reproducible.
The page should make the builder feel powerful while still being scientifically careful about limits.
PROTAC assembly is treated as a structured hypothesis, not simple molecule concatenation.
The workflow treats PROTAC design as component assembly constrained by geometry, not as simple concatenation of two ligands and a spacer.
Warhead, linker, and recruiter boundaries are preserved so downstream interpretation does not lose track of where each component begins and ends.
Attachment atoms and exit vectors are treated as first-class design choices because wrong anchors can invalidate otherwise attractive chemistry.
Assembled candidates are treated as hypotheses that need descriptor review, structural analysis, and experimental follow-up.
Inputs, component IDs, attachment logic, and outputs should be explicit enough that a workflow can be repeated, audited, and discussed later.
Builder output should be useful for modeling, scoring, batch workflows, reporting, and follow-up experimental design.
A visual rail for moving from component choice to exported candidate records.
Each component is a scientific decision, not just a dropdown value.
The warhead is the target-binding component. Bound pose and solvent exposure should guide modification-site choice, preserving target engagement rather than maximizing abstract modularity.
Linkers test bridgeability hypotheses. Length, polarity, attachment chemistry, rigidity, flexibility, and rotatable-bond burden should be documented rather than guessed implicitly.
Recruiter choice should consider bound pose, scaffold context, solvent exposure, attachment geometry, and the biological context of the recruited ligase.
A 2D-valid assembly can still be a poor 3D hypothesis when anchors are wrong.
Exit vectors describe how the linker leaves the warhead and recruiter. They matter because anchor choices can point a linker into a steric wall, destroy key binding interactions, or make an apparently valid molecule a weak ternary-complex hypothesis.
Parameterized routes create cleaner entry points for examples, documentation, teaching, and scripts.
Batch workflows should preserve enough metadata to make the run reproducible later.
API Builder and the public route surface support scriptable workflows where implemented. Methodologically, batch workflows should preserve component IDs, custom SMILES where relevant, attachment atoms, linker identifiers, query parameters, and output metadata.
What leaves the builder should be more than a string. It should be an interpretable candidate record.
Builder output is a hypothesis. No single computational score proves activity.
Downstream validation can include descriptor review, bridgeability checks, ternary modeling, molecular dynamics, ML re-ranking, and experimental degradation assays.
These pages connect methods to practical usage, component selection, automation, and downstream modeling.
Read user-facing scope, workflow, API, and troubleshooting answers.
Open FAQPractical assembly workflow from component choice to validation.
Read build guideSee how warheads, linkers, and recruiters connect into one workflow.
Open component hubsUpstream methodology for target-binding warhead inspection.
Open warhead guideBridgeability, linker classes, and geometry-aware linker thinking.
Open linker guideRecruiter-side structure, scaffold, and attachment-vector considerations.
Open recruiter guidePrepare batch-friendly and scripted workflows.
Open API BuilderMove assembled candidates into modeling, scoring, and prioritization workflows.
Open downstream modelingReport workflows and results more reproducibly.
Open benchmarkingStart with the builder, review the practical guide, or move into API-oriented workflows when you need repeatable computational design.