ECOD

What is ECOD?

ECOD (Evolutionary Classification of protein Domains; Cheng et al., 2014) is a hierarchical classification of protein domains organized according to their evolutionary relationships. This resource groups PDB structures by homology of its protein domains. It is distinct from structure based classifications such as SCOP and CATH because it focuses on remote homology of protein domains and is kept current by classifying newly released structures in the PDB archive.
Protein domains are grouped into five levels as described below:

• (A) architecture: groups protein domains with similar secondary structure compositions and geometric shapes
• (X) possible homology: groups protein domains where there is some evidence to demonstrate homology (but further verification is needed)
• (H) homology: groups proteins domains with common ancestry - as suggested by high sequence-structure scores, functional similarity, and shared unusual features
• (T) topology: groups protein domains with similar topological connections
• (F): family: groups protein domains with significant sequence similarity (according to Pfam and HHsearch-based clustering)

Why use the ECOD Browser?

Using this browser you can identify structures with homologous protein domains to reveal distant evolutionary relationships, especially ones that may not be evident from sequence and/or structure homology analyses. Such explorations may provide insights about the structures and functions of related proteins,.

How to use the ECOD Browser?

If you know something about the homology or domain of the protein of interest, use the ECOD browser to identify proteins of a specific architecture, homology, or family of interest. Alternatively, if you have a protein/domain name, you can type the name in the search box at the top of the page and select from the options in the autocomplete list.

After locating the individual or protein group of interest in the browser, users can view the number of PDB structures in this group. Clicking on the numbers listed next to the process name will launch a search for the PDB structures that have the ECOD domain of interest.

Examples

• Navigate through the tree and its branches for “A: alpha arrays” >> “X: Globin-like (From Topology)” >> “H: Globin-like (From Topology)” >> "T: Globin-like" and "F: Globin" OR
• Type a family name e.g., globin or GFP in the search box on the top of the page. Select from the autocomplete suggestions presented

References:

• 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 https://doi.org/10.1371/journal.pcbi.1003926
• H. Cheng, Y. Liao, R. D. Schaeffer, N. V. Grishin. (2015) Manual classification strategies in the ECOD database. Proteins 83(7): 1238-1251 https://doi.org/10.1002/prot.24818