> ## Documentation Index
> Fetch the complete documentation index at: https://docs.adaptyvbio.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Improve Protein Expression

> Practical strategies to get your proteins expressing better on our platform

## Common sequence issues to fix early

* Unpaired cysteines can create unwanted disulfides. Remove or pair them unless they are functionally required.
* High hydrophobic content and long hydrophobic patches often drive aggregation. Prefer balanced hydropathy and short, flexible linkers between domains.

## Recommended solubility and stability predictors

* [NetSolP](https://services.healthtech.dtu.dk/service.php?NetSolP-1.0): fast sequence-based solubility screen for triage.
* [SoluProt](https://loschmidt.chemi.muni.cz/soluprot/): predicts soluble expression in E. coli from sequence features.
* [SolubleMPNN](/wiki/models/solublempnn): solubility‑oriented variants of ProteinMPNN for redesigning constructs toward higher solubility (commonly used as a default starting point in redesign). See also [ProteinMPNN](/wiki/models/proteinmpnn).
* [ESM](/wiki/models/esm): use sequence log‑likelihoods to deprioritize hard‑to‑express variants.
* [ipTM](/wiki/models/iptm) ([AlphaFold‑Multimer](/wiki/models/alphafold-multimer)): interface quality metric that can correlate with complex stability in binder design workflows.
* [pSAE](/wiki/models/psae): exposure‑based measures (e.g., percent solvent‑accessible exposed hydrophobicity) are useful for ranking aggregation risk; implementations vary across toolkits.

<Tip>
  Definitions and references: [SolubleMPNN](/wiki/models/solublempnn), [ProteinMPNN](/wiki/models/proteinmpnn), [ESM](/wiki/models/esm), [ipTM](/wiki/models/iptm), [AlphaFold‑Multimer](/wiki/models/alphafold-multimer), [pSAE](/wiki/models/psae).
</Tip>

<Callout>
  Workflow: Filter with NetSolP/SoluProt → rank by ESM log‑likelihoods → redesign with SolubleMPNN‑style constraints → re‑screen.
</Callout>

## See also

* [Supported Protein Formats](/docs/experiment-setup/supported-protein-formats)
* [Creating Experiments](/docs/experiment-setup/creating-experiments)