Tutorials

Short step-by-step guides to get the most out of Visual PROTAC. Start with PROTAC Molecular Weight and the Linker Library, then use the 3D viewer for ternary complex or component structures.

• PROTAC Molecular Weight (linker)

  Enter warhead, linker, and E3 ligand as SMILES. Get combined molecular weight (with 2×H₂O connection loss), logP, TPSA, and per-moiety MW. Download a PDF report. Use the Linker Library to copy linker SMILES into this tool.

• Linker Library

  Browse common linkers (PEG, cleavable, alkyl, etc.) with SMILES, MW, and logP. Click "Use in Properties" to open the PROTAC Molecular Weight tool with that linker pre-filled. Use for design and to compare linker options.

• Physicochemical Properties

  Enter a peptide or protein sequence to get pI, molecular weight, charge, GRAVY. Use when your warhead or tag is peptide-based, or for stability/solubility checks. For full PROTAC (warhead–linker–E3) use PROTAC Molecular Weight.

• Ternary Complex Assembly

  Load a PDB of the ternary complex (target–PROTAC–E3) or assemble components. View in 3D, then export coordinates (PDB) or a screenshot (PNG) from the viewer sidebar. See Complex Export for workflow details.

• Component Alignment

  Upload your own complex or component PDB file. View and export the structure as PDB or PNG. Use when you have a local structure from modeling or a collaborator.

• Linker Conformation

  Multi-frame trajectory or conformation playback. Use to preview linker flexibility or conformational diversity. Export frames or PNG as needed.

Getting Started · PROTAC Design · PROTAC Examples · Complex Export · FAQ