Warhead discovery
Start from target-binding chemistry, protein-bound context, and attachment-aware warhead exploration before you commit to assembly.
Explore warheads
Schurer Lab Degrader Design
PROTAC Builder - Free In Silico Degrader Design Tool
PROTAC Builder is a free, server-rendered web application for assembling warheads, linkers, and E3 ligase recruiters into candidate degraders.
Design starts with components. PROTAC Builder helps turn warheads, linkers, and E3 recruiters into structured degrader hypotheses for downstream modeling, workflow handoff, and experimental planning.
Within the broader Schurer Lab ecosystem, Warhead Hunter supports warhead discovery, E3 Ligandalyzer supports recruiter and scaffold exploration, V-LiSEMOD supports viral protein-ligand and solvent-exposed moiety discovery for viral-target warhead development, and PROTAC Builder brings those component choices together for assembly.
🧬 Warhead + linker + E3 workflow
⚡ Browser-based assembly
🛰️ API-ready handoff
🧪 Validation-first design
Three-part PROTAC design workflow
A practical degrader design session starts with a target-binding warhead, an E3 ligase recruiter, and a linker that can bridge the two without forcing impossible geometry.
PROTAC Builder focuses on the assembly step: standardizing components, editing attachment atoms, generating merged structures, and preparing outputs for additional scoring, filtering, or structural modeling.
Linker design
Review linker length, polarity, flexibility, and bridgeability concepts before turning a component idea into a serious PROTAC hypothesis.
Explore linkersE3 recruiter discovery
Compare recruiter classes, attachment vectors, ligase-side geometry, and recruiter fit before pairing them with the target-facing warhead.
Explore recruitersConnected discovery ecosystem
The site does not pretend to be a complete standalone library for every warhead, recruiter, or context dataset. Instead, it links cleanly into the sister tools that go deeper in each area.
Warhead Hunter
Explore target-binding warheads, example jobs, and warhead-focused discovery workflows before bringing a candidate warhead back into assembly.
Explore warheads in Warhead Hunter ↗E3 Ligandalyzer
Inspect E3 recruiters, ligases, scaffolds, and recruiter attachment context before choosing the ligase-side anchor for a candidate degrader.
Inspect E3 recruiters in Ligandalyzer ↗V-LiSEMOD
Explore viral protein structures with bound ligands and solvent-exposed moieties that may support viral-target warhead discovery.
Explore viral warhead leads in V-LiSEMOD ↗Return to PROTAC Builder
Bring chosen components back into the builder for degrader assembly, workflow export, and downstream modeling handoff.
Return to PROTAC BuilderLearn, benchmark, and operationalize
What is a PROTAC?
Foundational explanation of targeted protein degradation, degrader anatomy, and what makes PROTACs different from simple inhibitors.
Open explainerHow to build a PROTAC
Step-by-step guidance covering component selection, attachment points, linker choices, and downstream-ready export thinking.
Read build guideIn silico PROTAC modeling
Overview of restrained docking, refinement, scoring, and hybrid workflows for evaluating assembled candidates more rigorously.
Explore modelingExamples
Browse launchable examples for target-ligand, CRBN, VHL, custom SMILES, API, and handoff-oriented workflows.
Open examples