Supplementary materials for "MemConverter: An Iterative Pipeline for Reprogramming Protein Localization in Membrane or Aqueous Solution"

Description

This dataset contains 85,051 isolated transmembrane domains derived from the tmAFDB and TED. It was specifically curated to fine-tune ProteinMPNN for membrane protein design (MemProtMPNN).

We focused on isolated domains to ensure the model learns specific membrane topological constraints rather than soluble features.

Data Construction

• Domain Extraction: Primarily based on domain annotations from The Encyclopedia of Domains (TED). For proteins without TED annotations, Merizo was used to identify domains.

• Filtering: Validated by TMbed. We excluded proteins with <20% transmembrane residues or domains shorter than 32 residues.

• Splitting: Clustered using MMseqs2 (30% sequence identity) to strictly separate Training, Validation, and Test sets.

Statistics

Files Description

• membrane_domain_dataset.zip: The main dataset archive.
  

• data_files.zip: Contains the processed dataset partitions (Train, Validation, Test). 

• test_list: A curated list of representative cases from the test set (one representative sequence per cluster) used for performance evaluation.