AlphaPulldown v2.1.0

[DimaMolod]

Release notes

• AlphaFold3 data pipeline support: You can now generate AlphaFold3-compatible data.json feature files directly from FASTA files for proteins, DNAs and RNAs using the create_individual_features.py script with the --data_pipeline flag.

• Support for all AlphaFold3 feature types: The pipeline now accepts all types of AlphaFold3 data.json feature files—including proteins, proteins with PTMs, DNA, RNA, and ligands. Place these files in the features directory and ensure they have a .json extension when using run_multimer_jobs.py or run_structure_prediction.py.

• AlphaFold2 and AlphaFold3 compatibility: You can now mix AlphaFold2 .pkl features (including "chopped" proteins defined with residue ranges) and AlphaFold3 .json features in the same prediction run.

---

This discussion was created from the release AlphaPulldown v2.1.0.