Evolutionary Classification of Protein Domains

Browse ECOD AF2/PDB combined classification as a tree or download distributable files. This classification currently includes both experimental structures and predicted models.

(2024/09/14) -- If you are looking for the original PDB-only ECOD (versions up to 291), that can still be found here

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ECOD is a hierarchical classification of protein domains according to their evolutionary relationships. This database contains our combined classification of structure predictions from 48 proteomes from AlphaFold Database with experimental structures from the Protein Data Bank. Previous versions of ECOD that solely classified the PDB are available here. Addtionally, published classifications of human, Vibrio parahaemolyticus, Salmonella enterica typhi and the original 48 proteomes are available.

Please cite the following references:

R. D. Schaeffer, K. E. Medvedev, et. al. (2024) ECOD: Integrating classifications of protein domains from experimental and predicted structures. NAR Submitted

R. D. Schaeffer, Y. Liao, H. Cheng, N. V. Grishin. (2017) ECOD: new developments in the evolutionary classification of domains. Nucleic Acids Res. 45(D1): D296-D302.

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.

ECOD statistics
410,427Predicted structures
201,228Experimental structures
718,390Experimental proteins/chains
1,816,770Domains
2,457X-groups
3,716H-groups
3,950T-groups
16,299F-groups
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