Related Experiment Video
Updated: Apr 11, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
70.1K
Using homology relations within a database markedly boosts protein sequence similarity search
Jing Tong1, Ruslan I Sadreyev2, Jimin Pei3
1Department of Molecular Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050;
Summary
This study introduces COMPADRE, a novel method for protein homology search that leverages known relationships between protein sequences. COMPADRE significantly improves detection accuracy, aiding in the prediction of protein structure and function.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Protein sequence homology inference is crucial for understanding protein structure, function, and evolution.
- Existing sequence-based methods often fail to detect similarities visible in protein structures.
- Integrating network relationships can enhance search engine performance.
Purpose of the Study:
- To develop a novel protein homology search method that improves accuracy by incorporating database relationships.
- To enhance the detection of structural similarities missed by traditional sequence-based approaches.
- To enable structure and function predictions for uncharacterized proteins.
Main Methods:
- Developed COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships), a new homology search algorithm.
- Assessed relationships between query and database sequences by analyzing similarities with known homologs.
- Applied network-based relationship analysis to protein sequence homology searching.
Main Results:
- COMPADRE significantly enhanced search accuracy, increasing the precision rate from 18% to 83% at half-coverage.
- The method successfully detected a substantial fraction of protein structural relationships.
- Achieved improved detection of homology for previously uncharacterized proteins.
Conclusions:
- The COMPADRE method offers a significant advancement in protein homology inference accuracy.
- Incorporating database relationships is a powerful strategy for improving biological similarity detection.
- This approach facilitates structure and function prediction, advancing protein research.
Related Concept Videos
02:47Protein Families
17.6K
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...
17.6K
02:47Protein Families
4.7K
4.7K
02:54Evolutionary Relationships through Genome Comparisons
7.3K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.3K
01:57Gene Families
10.3K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
10.3K
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
01:54Convergent Evolution
34.6K
Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
34.6K