Related Experiment Video
Updated: Jun 23, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Improving protein structure similarity searches using domain boundaries based on conserved sequence information.
Kenneth Evan Thompson1, Yanli Wang, Tom Madej
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA. EvanThompson@jhu.edu
BMC Structural Biology
|May 21, 2009
Summary
Defining protein domains using conserved sequence alignments improves structure similarity searches. This approach enhances the Vector Alignment Search Tool (VAST) and protein structure comparisons.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein domain identification is crucial for protein structure comparison.
- Current methods use structurally compact domains for algorithms like Vector Alignment Search Tool (VAST).
- Investigating alternative domain definitions based on sequence conservation is needed.
Purpose of the Study:
- To evaluate the impact of sequence-derived domain definitions on VAST performance.
- To compare structure-based versus sequence-based domain boundaries in similarity searches.
Main Methods:
- Utilized curated protein sequence domain families from the Conserved Domain Database (CDD).
- Identified alternative domains based on alignment footprints.
- Analyzed domain boundary discrepancies in the Molecular Modeling Database (MMDB).
Main Results:
- Alternative domains showed different secondary structure compositions compared to compact units.
- Domain boundary definitions differed for approximately 8% of protein chains.
- Sequence-based domain boundaries slightly outperformed structure-based domains in similarity searches, with notable improvements in some cases.
Conclusions:
- Sequence-based domain boundaries offer a valuable method for identifying protein structure similarities.
- The improved performance necessitates integrating sequence domain boundaries into VAST and MMDB.
- This integration will enhance protein structure comparison capabilities within the NCBI Entrez system.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
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 form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:49Conserved Binding Sites
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 analyses the...
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 analyses the...
01:49Conserved Binding Sites
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 analyses the...
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 analyses the...
02:26Conservation of Protein Domains
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 form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview