Name Uploaded Size
▶ v3
▶ v6

Readme

AlphaFold cluster produced by our novel foldseek structural clustering algorithm. We clustered the AlphaFold database into 2.27M non-singleton structural clusters. On this site we provide the cluster data.

Barrio-Hernandez I, Yeo J, Jänes J, Wein T, Varadi M, Velankar S, Beltrao P, Steinegger M. Clustering predicted structures at the scale of the known protein universe. bioRxiv doi: doi.org/10.1101/2023.03.09.531927 (2023)

Foldseek Marv

Updates

  • 2026-08-10: v6 7-AFDB50-repId_memId.tsv.gz is added. The cluFlag column in the v6 file 1 and file 5 is corrected. Data previews are now shown for the v3 and v6 files in the Data description section below.
  • 2026-03-27: repLen of the v6 file 2 is updated. ava data of the v6 file (file no. 6) is updated
  • 2026-03-21: TaxLCA of the v6 file 2 is updated.
  • 2026-03-10: The cluster flag information is amended for v6.
  • 2026-03-04: The update of the AFDB v6. The AFDB Clusters - rep-member (no. 1), cluster information (no. 2), the whole clusters rep-mem (no. 5) and the all-vs-all alignment of the AFDB Cluster representative information are updated.
  • 2025-09-12: share_db/8-cluster_alignment_tmscore_lddt.tar.gz is added. The alignment information of the AFDB Clusters
  • 2024-12-16: 6-all-vs-all-similarity-queryId_targetId_eValue-Dec16_2024.tsv.gz is added. The representative ids were substituted and e-value has changed
  • 2024-12-13: 7-AFDB50-repId_memId.tsv.gz is added.
  • 2024-12-03: 6-all-vs-all-similarity-queryId_targetId_eValue-Dec3_2024_updated.tsv.gz is added. The representative ids were substituted
  • 2023-06-05: 6-all-vs-all-similarity-queryId_targetId_eValue.tsv.gz is added
  • 2023-05-25: Erroneous merge in fragment removal step was solved. cluFlag column is added to file 3 so that all of the human proteins
  • 2023-03-19: 5-allmembers-repId-entryId-cluFlag-taxId.tsv.gz is added. Now it is available to see all mapping information of AFDB. The identifiers in file 1, 2 and 3 are removed.

Website

For an interactive view on a subset of the data please check out our website here.

Data description

v3 v6
1-AFDBClusters-entryId_repId_taxId.tsv.gz  — AFDB clusters' information
  1. memberID identifier of member in cluster
  2. repId identifier of the representative
  3. taxId the taxonomy ID of the member

Preview

A0A009E921 A0A009E921 1310605 A0A009F5K6 A0A009E921 1310605 A0A009E9H3 A0A009E9H3 1310605 A0A484ZLT0 A0A009E9H3 82979 A0A009ECR5 A0A009ECR5 1310605
2-repId_isDark_nMem_repLen_avgLen_repPlddt_avgPlddt_LCAtaxId.tsv.gz  — Cluster overview
  1. repID: ID of the representative protein in the Foldseek cluster
  2. isDark: whether the protein is from a dark proteome (0 = not dark, 1 = dark)
  3. nMem: number of members in the Foldseek cluster without fragments
  4. repLen: length of the representative protein sequence
  5. avgLen: average length of the protein sequences in the Foldseek cluster
  6. repPlddt: pLDDT score of the representative protein structure
  7. avgPlddt: average pLDDT score of the protein structures in the Foldseek cluster
  8. LCAtaxID: taxonomy ID of the lowest common ancestor (LCA) of the proteins in the Foldseek cluster

Preview

A0A6A4IZ81 0 4 386 387.25 89.69 91.1875 131567 A0A6M1CKG1 0 3 122 122.667 96.06 88.1467 91347 A0A4Q3Q6P1 1 3 117 113.333 71.94 67.8333 80864 A0A4V3EFQ4 0 3 153 156 68.56 58.8533 131567 A0A4V3EKB1 1 3 51 51 62.62 62.77 1883
3-sapId_sapGO_repId_cluFlag_LCAtaxId.tsv.gz  — Human cluster
  1. human ID: ID of the human protein
  2. GOs: Gene Ontology terms associated with the protein
  3. rep ID: ID of the representative protein if the human protein is clustered in the Foldseek clustering step
  4. cluFlag 1: clustered in AFDB50, 2: clustered in AFDB clusters, 3: removed (fragments in Foldseek clusters), 4: removed (singletons in Foldseek clusters)
  5. LCA taxonomy ID: LCA taxonomy ID of the cluster where the human protein is assigned

Preview

J3KRM4 GO:0016021;GO:0015267; A0A013RMH7 3 131567 C9J222 GO:0043229;GO:0003677;GO:0003887;GO:0006281; A0A014PHZ8 3 2759 C9JF34 GO:0043229;GO:0003677;GO:0003887;GO:0006281; A0A014PHZ8 1 2759 Q6ZS12 GO:0016021;GO:0005886;GO:0022839;GO:0005267; A0A015IFA8 1 33154 V9GYA4 GO:0003700;GO:0008630;GO:0000122; A0A015JSV1 3 N/A
4-domain-clustering.zip  — Domain analysis related files

Domain analysis related files

5-allmembers-repId-entryId-cluFlag-taxId.tsv.gz  — Cluster information of 214M AFDB sequences
  1. repId identifier of the representative
  2. memId identifier of the member - AFDB sequences
  3. cluFlag 1: clustered in AFDB50, 2: clustered in AFDB clusters, 3: removed (fragments in Foldseek clusters), 4: removed (singletons in Foldseek clusters)
  4. taxId the taxonomy ID of the member

Preview

A0A009DWC5 A0A009DWC5 3 1310605 A0A009DWD5 A0A009DWD5 3 1310605 A0A009DWF0 A0A009DWF0 3 1310605 A0A009DWH9 A0A009DWH9 3 1310605 A0A009DWL0 A0A009DWL0 4 1310605
6-all-vs-all-similarity-queryId_targetId_eValue.tsv.gz  — Cluster similarity e-value
  1. queryId identifier of the query
  2. targetId identifier of the target
  3. e-value similarity e-value

Preview

S4YGI1 S4YGI1 2.211E-42 S4YGI1 A0A017T8V7 1.886E-13 S4YGI1 A0A1M3NHW0 3.298E-07 S4YGI1 A0A857JKL2 1.318E-02 S4YGI1 A0A136PAL6 4.846E-01
7-AFDB50-repId_memId.tsv.gz  — Sequence clusters AFDB50
  1. repId identifier of the representative
  2. memId identifier of the member - AFDB50 sequence

Preview

A0A5C6TQW4 A0A2U0VG77 A0A5C6TQW4 A0A853FKP6 A0A5C6TQW4 A0A1Y2QK75 A0A5C6TQW4 A0A1Q4DVP5 A0A5C6TQW4 A0A7X5ZUI3
8-cluster_alignment_tmscore_lddt.tar.gz  — Alignment of AFDB Clusters
  1. aln-query_target_fident_alnlen_mismatch_gapopen_qstart_qend_tstart_tend_evalue_bits_lddt_alntmscore.tsv: Alignment of AFDB Clusters - members to their representative
  2. lddt-repId_sumLddt_nMem_avgLddt.tsv: Average lddt computed
  3. tmScore-repId_sumLddt_nMem_avgLddt.tsv: Average TM-Score computed
commands.gz  — Script used for analysis

Script used to analysis

1-AFDBClusters-repId_entryId_cluFlag_taxId.tsv.gz  — AFDB clusters' information
  1. repId identifier of the representative
  2. entryId identifier of member in cluster
  3. cluFlag 1: clustered in AFDB clusters (Foldseek), 2: clustered in AFDB50 (MMseqs)
  4. taxId the taxonomy ID of the member

Preview

L2GK61 L2GK61 1 993615 L2GK61 A0A820QN40 1 433720 A0A377JXT1 A0A377JXT1 1 562 A0A377JXT1 A0AAW7VL20 1 562 A0A0C2YUD9 A0A0C2YUD9 1 1036808
2-repId_isDark_nMem_repLen_avgLen_repPlddt_avgPlddt_LCAtaxId.tsv.gz  — Cluster overview
  1. repID: ID of the representative protein in the Foldseek cluster
  2. isDark: whether the protein is from a dark proteome (0 = not dark, 1 = dark)
  3. nMem: number of members in the Foldseek cluster
  4. repLen: length of the representative protein sequence
  5. avgLen: average length of the protein sequences in the Foldseek cluster
  6. repPlddt: pLDDT score of the representative protein structure
  7. avgPlddt: average pLDDT score of the protein structures in the Foldseek cluster
  8. LCAtaxID: taxonomy ID of the lowest common ancestor (LCA) of the proteins in the Foldseek cluster

Preview

A0A522E0C9 1 2 73 76.6667 70.5 73.94 0 A0A924B8Z5 0 5 173 161.318 72.12 94.8553 2 A0A7I4YSJ4 0 8 120 126.4 62.69 68.378 6236 A0A947S9J0 1 12 292 283.062 77.38 72.9294 1783234 A0A291RMX2 0 75 169 174.457 89.69 83.5313 2
5-allmembers-repId-entryId-cluFlag-taxId.tsv.gz  — Cluster information of 214M AFDB sequences
  1. repId identifier of the representative
  2. memId identifier of the member - AFDB sequences
  3. cluFlag 1: clustered in AFDB clusters (Foldseek), 2: clustered in AFDB50 (MMseqs)
  4. taxId the taxonomy ID of the member

Preview

A0AAZ3QHE7 A0AAZ3QHE7 1 74940 A0A7V8DG14 A0A7V8DG14 1 0 A0A060CI31 A0A060CI31 1 0 A0A060ZM91 A0A060ZM91 1 576784 A0A644Z1U6 A0A644Z1U6 1 1076179
6-all-vs-all-similarity-queryId_targetId_eValue.tsv.gz  — Cluster similarity e-value
  1. queryId identifier of the query
  2. targetId identifier of the target
  3. e-value similarity e-value

Preview

A0A7W9CT64 A0A7W9CT64 1.590E-07 A0A7W9CT64 A0A498GXR6 1.141E-02 A0A7W9CT64 A0A7L2L0B1 3.894E-02 A0A7W9CT64 A0A7W1K2F4 3.894E-02 A0A7W9CT64 A0A7C4BYV0 8.662E-01
7-AFDB50-repId_memId.tsv.gz  — Sequence clusters AFDB50
  1. repId identifier of the representative - AFDB50 sequence
  2. memId identifier of the member - AFDB50 sequence

Preview

AF-A0A8B7NY52-F1-model_v6 AF-A0A8B7NY52-F1-model_v6 AF-A0AA36DYN6-F1-model_v6 AF-A0AA36DYN6-F1-model_v6 AF-A0AAU2HJX9-F1-model_v6 AF-A0AAU2HJX9-F1-model_v6 AF-A0A660WT05-F1-model_v6 AF-A0A660WT05-F1-model_v6 AF-A0AAN8SFE2-F1-model_v6 AF-A0AAN8SFE2-F1-model_v6 AF-A0AAN8SFE2-F1-model_v6 AF-E0VRJ2-F1-model_v6

License

All files are available under a Creative Commons Attribution 4.0 International License.