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The Evolutionary Classification of Protein Domains (ECOD) is a biological database that classifies protein domains available from the Protein Data Bank. The ECOD tries to determine the evolutionary relationships between proteins.
| Content | |
|---|---|
| Data types captured | Protein domains |
| Contact | |
| Research center | Grishin Lab, University of Texas Southwestern Medical Center |
| Authors | H. Cheng, R. D. Schaeffer, Y. Liao, L. N. Kinch, J. Pei, S. Shi, B. H. Kim, N. V. Grishin. |
| Primary citation | PMID 25474468 |
| Release date | 2014 |
| Access | |
| Website | http://prodata.swmed.edu/ecod/ |
| Miscellaneous | |
| Version | continuously updated |
| Curation policy | manual for new proteins; automated for ones with close matches |
Similar to Pfam, CATH, and SCOP, ECOD compiles domains instead of whole proteins. However, ECOD focuses on evolutionary relationships more heavily: instead of grouping proteins by folds, which may simply represent convergent evolution, ECOD groups proteins by demonstratable homology and then by detailed topology and protein families[1]
The database uses a five-level hierarchy to categorize protein domains from broad shapes down to specific families:
- (A) Architecture: The highest level, grouping domains by similar secondary structure compositions and geometric arrangements (e.g., alpha bundles or beta sandwiches).
- (X) Possible Homology: Clusters domains that share structural similarity where homology is suspected but not yet definitively proven.
- (H) Homology: The core level of the database, grouping domains with strong evidence of common ancestry based on sequence-structure scores and functional similarity.
- (T) Topology: Groups domains with similar topological connections. This level recognizes that homologous proteins can sometimes evolve different folds.
- (F) Family: The most specific level, grouping domains with significant sequence similarity, often based on Pfam classifications.
ECOD has been applied to a subset of the AlphaFold Database (protein sequences in SwissProt)[2].
References
edit- ↑ Cheng, H; Schaeffer, RD; Liao, Y; Kinch, LN; Pei, J; Shi, S; Kim, BH; Grishin, NV (December 2014). "ECOD: an evolutionary classification of protein domains". PLOS Computational Biology. 10 (12) e1003926. Bibcode:2014PLSCB..10E3926C. doi:10.1371/journal.pcbi.1003926. PMC 4256011. PMID 25474468.
- ↑ Schaeffer, RD; Zhang, J; Cong, Q; Grishin, NV (March 2026). "ECOD: Classification of domains in AFDB Swiss-Prot structure predictions". PLoS computational biology. 22 (3): e1013431. doi:10.1371/journal.pcbi.1013431. PMID 41911251.
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