---
title: PROTAC troubleshooting
description: >-
  Resolve linker enumeration failures, ternary complex modeling errors, and
  degradation scoring issues.
tags:
  - protac
  - troubleshooting
---

## PROTAC troubleshooting

This page helps you diagnose failures across the [PROTAC](/docs/protac) design pipeline — invalid warhead or E3 ligand SMILES, linker enumeration that returns too few candidates, ternary complex modeling errors, low feasibility scores, weak degradation predictions and hook-effect risk, and GPU job timeouts.

## Invalid warhead or E3 ligand SMILES

**Symptom**: "Invalid SMILES" or "Failed to parse structure" error during linker enumeration.

**Fixes**:

- Validate your SMILES using a structure editor or RDKit before submission
- Check for unmatched parentheses, brackets, or ring closure digits
- Ensure stereochemistry notation is correct (especially for VHL ligands with hydroxyproline)
- Remove salts or counterions from the SMILES -- provide only the parent structure
- Maximum fragment size is 200 heavy atoms. If your warhead or E3 ligand exceeds this, simplify the structure

## Linker enumeration returns zero or very few linkers

**Symptom**: Fewer linkers generated than requested.

**Fixes**:

- Widen the linker length range. If `min_linker_length` and `max_linker_length` are too close (e.g., both 6), there may not be enough chemical space to fill
- Increase `sa_threshold` to allow less synthetically accessible linkers (default 5.0, try 7.0)
- Increase `max_rotatable_bonds` to allow more flexible linkers
- Switch `scaffold_type` from a specific type to `"diverse"` for more options
- Check that the warhead and E3 ligand SMILES have accessible attachment points. If the exit vectors are buried in a ring system, linker attachment may fail

## Ternary complex modeling fails

**Symptom**: "Complex modeling failed" or timeout error.

**Fixes**:

- Verify the PDB ID is correct and contains the expected protein chain
- If using an uploaded structure, ensure it is a valid PDB or mmCIF file with proper chain and residue numbering
- The E3 ligase structure should include the full binding domain. For CRBN, include DDB1; for VHL, include ElonginB and ElonginC
- Reduce `num_conformers` if the job times out (try 5 instead of 10)
- Increase `clash_tolerance` if the modeler reports excessive clashes (try 3.0 instead of 2.0)
- Check that the PROTAC SMILES matches the warhead and E3 ligand used in the structure files

## All ternary conformers have low feasibility scores

**Symptom**: Feasibility scores below 0.4 for all conformers.

**Fixes**:

- The linker may be too short or too long for the distance between binding sites. Try a different linker length range
- The exit vectors of the warhead and E3 ligand may be geometrically incompatible. Try rotating the attachment point or using a different warhead binding pose
- Some POI-E3 ligase pairs have unfavorable protein-protein interfaces regardless of linker. This is a genuine biological result, not a tool error
- Try a different E3 ligase system (switch from CRBN to VHL or vice versa)

## Degradation score shows high hook effect risk

**Symptom**: Hook effect risk reported as "high."

**Fixes**:

- The hook effect is driven by high binary binding affinities relative to ternary complex stability. This is a molecular property, not a tool error
- Reduce warhead affinity slightly (if possible) to favor ternary complex formation
- Increase linker rigidity to stabilize the ternary complex (use triazole or piperazine scaffolds)
- Increase cooperativity by optimizing the POI-E3 protein-protein interface (use ternary modeling to guide this)
- In practice, the hook effect primarily matters at high concentrations (> 1 uM). If your target DC50 is < 100 nM, the hook effect may not be clinically relevant

## Degradation score reports DC50 > 10 uM

**Symptom**: Predicted DC50 in the micromolar range, grade D or F.

**Fixes**:

- Check the ternary complex feasibility first. Poor ternary complex geometry is the most common cause of weak degradation
- Ensure the warhead has sufficient binding affinity to the POI. A weak binder (Kd > 1 uM) will produce a weak degrader
- Try a different E3 ligase system. Some targets are better degraded via CRBN than VHL, or vice versa
- Optimize the linker: length, flexibility, and attachment point all affect degradation efficiency
- If `ternary_job_id` was not provided, supply it for more accurate predictions incorporating 3D geometry

## Job timeout or GPU error

**Symptom**: "Job failed: timeout" or "GPU allocation failed."

**Fixes**:

- Linker enumeration with `num_linkers > 100` may take over 2 minutes. Reduce the count or split into multiple runs
- Ternary modeling with `num_conformers > 20` is computationally expensive. Use 10 conformers for initial screening
- If GPU allocation fails, retry after a few minutes. Peak usage can cause temporary queuing
- Very large protein structures (> 1000 residues) increase modeling time. Trim the PDB to include only the relevant domain

## Getting help

If issues persist:

1. Check the tool error message for specific parameter suggestions
2. Validate SMILES strings independently using RDKit or a structure editor
3. Verify PDB structures are complete and contain the expected chains
4. Describe the issue to Ivy

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