Quick Start
Build a PROTAC from three modular pieces
PROTAC Builder helps you assemble a degrader by combining a
warhead / target ligand, a linker,
and an E3 ligase recruiter.
Warhead
Select from V-LiSEMOD, paste a SMILES, or draw/edit your own
target-binding ligand.
Linker
Choose a curated linker, filter by properties, paste a SMILES,
or design one manually.
Ligase
Select or load an E3 ligase recruiter, then define where the linker
should attach.
Attachment Atom Cheat Sheet
Mark the connection points before saving
-
Warhead:
add a bonded
U atom at the warhead attachment site.
-
Linker:
add
U at the warhead-facing end and V
at the ligase-facing end.
-
Ligase recruiter:
add a bonded
V atom at the ligase recruiter attachment site.
After editing each panel, click Save under Warhead,
Linker, and Ligase Recruiter. Then click Generate PROTAC.
Loading Molecules
Use SMILES when you already know the structure
Click Load from SMILES under the Warhead, Linker,
or Ligase Recruiter panel, paste a valid SMILES string, and load it
into the editor.
Once loaded, you can modify the molecule, add the required
U/V attachment atom, and click
Save.
Companion Tools
Use the discovery tools when you need help choosing components
-
Warhead Hunter:
helps identify or import target-binding warheads.
-
E3 Ligandalyzer:
helps explore E3 ligase recruiter options.
-
V-LiSEMOD:
provides selectable warheads from the builder dropdown.
Shareable Builder Links
Open PROTAC Builder with molecules already loaded
Advanced users can create links that preload a warhead, linker,
or ligase recruiter.
Builder
https://protacbuilder.com/builder
Warhead SMILES
https://protacbuilder.com/builder?smiles=ENCODED_WARHEAD_SMILES
Linker SMILES
https://protacbuilder.com/builder?linker=ENCODED_LINKER_SMILES
Ligase Recruiter
https://protacbuilder.com/builder?ligase=LIGASE_NAME
Multiple Pieces
https://protacbuilder.com/builder?smiles=WARHEAD_SMILES&linker=LINKER_SMILES&ligase=LIGASE_NAME
Developer Notes
Local testing and query parameter reference
Local development builder URL:
http://192.168.1.154:5069/builder
Supported warhead preload parameters:
?smiles=
?lig_smi=
?warhead_smiles=
?warheadSmiles=
Backend/database ligand preload:
/builder?ligand=YOUR_LIGAND_CODE
Real SMILES should be URL-encoded before being placed into a link:
encodeURIComponent(smiles)
const url =
"/builder?smiles=" +
encodeURIComponent(warheadSmiles) +
"&linker=" +
encodeURIComponent(linkerSmiles) +
"&ligase=" +
encodeURIComponent(ligaseName);