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alphafold life sciences msa open source software openfold protein protein folding protein template


Multiple sequence alignments (MSAs) for 132,000 unique Protein Data Bank (PDB) chains, covering 640,000 PDB chains in total, and 4,850,000 UniClust30 clusters. Template hits are also provided for the PDB chains and 270,000 UniClust30 clusters chosen for maximal diversity and MSA depth. MSAs were generated with HHBlits (-n3) and JackHMMER against MGnify, BFD, UniRef90, and UniClust30 while templates were identified from PDB70 with HHSearch, all according to procedures outlined in the supplement to the AlphaFold 2 Nature paper, Jumper et al. 2021. We expect the database to be broadly useful to structural biologists training or validating deep learning models for protein structure prediction and related tasks.

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CC BY 4.0


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How to Cite

OpenProteinSet was accessed on DATE from Additionally, please cite our manuscript.

Usage Examples


Resources on AWS

  • Description
    A repository of MSAs and template hits.
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    AWS Region
    AWS CLI Access (No AWS account required)
    aws s3 ls --no-sign-request s3://openfold/

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