Getting started with Visual PROTAC

What we offer

Enter warhead, linker, and E3 ligand (SMILES) to get combined molecular weight (with connection mass loss), logP, and TPSA. Browse the Linker Library for common linkers (PEG, cleavable, etc.) and plug them into the PROTAC MW tool. View ternary complex or component structures in 3D and export PDB or PNG. For peptide or sequence-derived properties use Physicochemical Properties. Export options: Export formats, Complex Export.

Typical workflow

1. PROTAC MW: Go to PROTAC Molecular Weight (linker), enter warhead, linker, and E3 ligand SMILES. Get combined MW, logP, TPSA, and a PDF report. Use Linker Library to pick linkers and copy SMILES.
2. 3D complex: Use Ternary Complex Assembly to load or assemble target–PROTAC–E3 PDB; export PDB or PNG. Use Component Alignment to load your own structure file.
3. Linker conformation: Use Linker Conformation to preview linker conformations in multi-frame mode.
4. Sequence properties: For pI, MW, or stability from a peptide sequence (e.g. tag or peptide warhead) use Physicochemical Properties.

Tools at a glance

• PROTAC Molecular Weight (linker) — Warhead + linker + E3 ligand (SMILES) → combined MW, logP, TPSA, PDF report.
• Linker Library — Common linkers with SMILES, MW, logP; use in PROTAC MW or copy for design.
• Physicochemical Properties — pI, MW, charge, GRAVY from peptide or sequence (e.g. peptide warhead).
• Ternary Complex Assembly — Load or assemble target–PROTAC–E3; view, export PDB/PNG.
• Linker Conformation — Multi-frame linker/conformation preview.
• Component Alignment — Upload PDB; view and export.

Export: Export, Export formats, Complex Export.

Docs and reference

• PROTAC Design Principles — Ternary complex, warhead, linker, E3 ligand.
• PROTAC Examples — Example molecules (ARV-771, dBET1, MZ1, etc.).
• Data sources — PROTAC-DB, PDB, ChEMBL.
• Tutorials — Step-by-step for PROTAC MW, Linker Library, 3D viewer.
• API — Programmatic access.

More questions? FAQ. About: About.