foldcomp

Foldcomp

Foldcomp compresses protein structures with torsion angles effectively. It compresses the backbone atoms to 8 bytes and the side chain to additionally 4-5 byes per residue, thus an averaged-sized protein of 350 residues requires ~6kb.

Foldcomp efficient compressed format stores protein structures requiring only 13 bytes per residue, which reduces the required storage space by an order of magnitude compared to saving 3D coordinates directly. We achieve this reduction by encoding the torsion angles of the backbone as well as the side-chain angles in a compact binary file format (FCZ).

Foldcomp currently only supports compression of single chain PDB files

Publications

Hyunbin Kim, Milot Mirdita, Martin Steinegger, Foldcomp: a library and format for compressing and indexing large protein structure sets, Bioinformatics, 2023;, btad153,

Presentation Video

We presented Foldcomp at ISMB/ECCB2023. Check it out:

Usage

Installing Foldcomp

# Install Foldcomp Python package
pip install foldcomp

# Download static binaries for Linux
wget https://mmseqs.com/foldcomp/foldcomp-linux-x86_64.tar.gz

# Download static binaries for Linux (ARM64)
wget https://mmseqs.com/foldcomp/foldcomp-linux-arm64.tar.gz

# Download binary for macOS
wget https://mmseqs.com/foldcomp/foldcomp-macos-universal.tar.gz

# Download binary for Windows (x64)
wget https://mmseqs.com/foldcomp/foldcomp-windows-x64.zip

Executable

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Downloading Databases

We offer prebuilt databases for multiple large sets of predicted protein structures and a Python helper to download the database files.

You can download the AlphaFoldDB Swiss-Prot with the following command:

python -c "import foldcomp; foldcomp.setup('afdb_swissprot_v4');

Currently we offer the following databases:

We skipped all structures with discontinuous residues or other issues.

• ESMAtlas full (v0 + v2023_02): foldcomp.setup('esmatlas')

• ESMAtlas v2023_02: foldcomp.setup('esmatlas_v2023_02')

• ESMAtlas high-quality: foldcomp.setup('highquality_clust30')

• AlphaFoldDB Uniprot

  • v6: foldcomp.setup('afdb_uniprot_v6')
  • v4: foldcomp.setup('afdb_uniprot_v4')

• AlphaFoldDB Swiss-Prot: foldcomp.setup('afdb_swissprot_v4')

• AlphaFoldDB Model Organisms: foldcomp.setup('h_sapiens')

  • a_thaliana, c_albicans, c_elegans, d_discoideum, d_melanogaster, d_rerio, e_coli, g_max, h_sapiens, m_jannaschii, m_musculus, o_sativa, r_norvegicus, s_cerevisiae, s_pombe, z_mays

• AlphaFoldDB Cluster Representatives: foldcomp.setup('afdb_rep_v4')

• AlphaFoldDB Cluster Representatives (Dark Clusters): foldcomp.setup('afdb_rep_dark_v4')

Version 6 of AlphaFoldDB subset will be available soon.

If you want other prebuilt datasets, please get in touch with us through our GitHub issues.

If you have issues downloading the databases you can navigate directly to our download server and download the required files. E.g. afdb_uniprot_v4, afdb_uniprot_v4.index, afdb_uniprot_v4.dbtype, afdb_uniprot_v4.lookup, and optionally afdb_uniprot_v4.source.

Python API

You can find more in-depth examples of using Foldcomp's Python interface in the example notebook:

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Subsetting Databases

If you are dealing with millions of entries, we recommend using createsubdb command of mmseqs2 to subset databases. The following commands can be used to subset the AlphaFold Uniprot DB with given IDs.

# mmseqs createsubdb --subdb-mode 0 --id-mode 1 id_list.txt input_foldcomp_db output_foldcomp_db
mmseqs createsubdb --subdb-mode 0 --id-mode 1 id_list.txt afdb_uniprot_v4 afdb_subset

Please note that the IDs in afdb_uniprot_v4 are in the format AF-A0A5S3Y9Q7-F1-model_v4 .

Community Contributions

• PyMOL Plugin for reading Foldcomp files by @yakomaxa

Contributor