Related Experiment Video
Updated: Apr 19, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
4.2K
ECOD: an evolutionary classification of protein domains
Hua Cheng1, R Dustin Schaeffer1, Yuxing Liao2
1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
Plos Computational Biology
|December 5, 2014
Summary
We created the Evolutionary Classification of protein Domains (ECOD) database, classifying protein structures by evolutionary relationships. ECOD highlights distant homologs, aiding protein evolution and function studies.
Area of Science:
- Structural biology
- Bioinformatics
- Evolutionary biology
Background:
- Understanding protein evolution offers insights into structure and function.
- Access to evolutionary information is crucial for research.
- Existing classifications may not fully capture evolutionary relationships.
Purpose of the Study:
- To develop a hierarchical evolutionary classification of all proteins with experimentally determined structures.
- To present this classification as an interactive and updatable online database called ECOD.
- To emphasize evolutionary relationships (homology) over topology for protein domain classification.
Main Methods:
- Developed a hierarchical classification system based on evolutionary relationships (homology).
- Grouped protein domains primarily by homology, distinguishing from topology-based classifications.
- Utilized an automated pipeline for consistent and rapid classification of weekly PDB structure releases.
Main Results:
- Created ECOD, an interactive and updatable online database classifying protein domains.
- ECOD classifies ~100,000 protein structures into 9,000 sequence families and ~2,000 evolutionary groups.
- ECOD uniquely identifies distantly related homologs, revealing more evolutionary links than other classifications.
Conclusions:
- ECOD provides a comprehensive evolutionary classification of protein domains.
- The database aids in understanding protein structure evolution by highlighting homology across different topologies.
- ECOD's emphasis on distant homologs and PDB synchronization offers unique advantages for biological and evolutionary studies.
More Related Videos
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
15.3K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
15.3K
02:26Conservation of Protein Domains
4.4K
4.4K
02:47Protein Families
17.7K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
17.7K
02:47Protein Families
4.7K
4.7K
01:21Three-Domain System of Life
2.5K
Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
2.5K
01:49Conserved Binding Sites
5.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.3K