Evolutionary Classification of Protein Domains

Browse ECOD classification as tree or download distributable files. The classification currently includes only proteins with experimentally determined spatial structures.

As of 2024, ECOD also offers provisional classifications of human, Vibrio parahaemolyticus RIMD, Salmonella enterica typhi, and 48 reference proteomes from the AlphaFold DB.

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ECOD was updated on Mon Mar 25 20:11:27 CDT 2024 and contains 207,142 PDB structures released before 10/20/2023.

ECOD is a hierarchical classification of protein domains according to their evolutionary relationships. Only proteins with experimentally determined spatial structures from the PDB database are currently classified in ECOD. Compared with other classification databases, such as SCOP and CATH, ECOD emphasizes on distant evolutionary relationships and updates every week to include new structures released in PDB. Due to the delay of PDB FTP release and time needed to classify new domains, ECOD usually falls two to three weeks behind the PDB.

Please cite the following reference:

H. Cheng, R. D. Schaeffer, Y. Liao, L. N. Kinch, J. Pei, S. Shi, B. H. Kim, N. V. Grishin. (2014) ECOD: An evolutionary classification of protein domains. PLoS Comput Biol 10(12): e1003926.

H. Cheng, Y. Liao, R. D. Schaeffer, N. V. Grishin. (2015) Manual classification strategies in the ECOD database. Proteins 83(7): 1238-1251.

ECOD statistics (history)
207,142PDBs
758,660PDB chains
1,083,021Domains
2,459X-groups
3,717H-groups
12,948F-groups
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