Related Experiment Video
Updated: Jul 10, 2026

16:24
Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs
Hua Cheng1, Bong-Hyun Kim, Nick V Grishin
1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.
Proteins
|October 13, 2007
Summary
We created MALIDUP, a unique database of protein domain structure alignments. This resource aids protein evolution studies and evaluates structure alignment tools, focusing on structural similarity over sequence.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein evolution
Background:
- Homologous protein domains often arise from internal duplication within a single polypeptide chain.
- Divergence in function and sequence is common for duplicated domains, complicating traditional homology detection.
- Existing databases may be biased by sequence or functional similarity, limiting their scope for structural analysis.
Purpose of the Study:
- To introduce MALIDUP (manual alignments of duplicated domains), a novel database.
- To provide a resource for studying structurally similar protein domains originating from internal duplication.
- To offer a benchmark for assessing the performance of automated structure alignment programs.
Main Methods:
- Manual curation of 241 pairwise structure alignments.
- Focus on homologous domains resulting from internal duplication events within proteins.
- Comparison of manual alignments with outputs from established automatic structure alignment tools.
Main Results:
- The MALIDUP database contains 241 manually curated pairwise structure alignments of duplicated domains.
- Manual alignments largely correspond with automatic structural alignments from common software.
- MALIDUP represents a dataset less biased by sequence or functional similarity compared to other homology databases.
Conclusions:
- MALIDUP is the first database specifically designed for structurally similar homologs derived from internal duplication.
- The database serves as a valuable resource for investigating protein evolution and domain duplication.
- MALIDUP provides a reliable reference set for the validation and improvement of protein structure alignment algorithms.
More Related Videos
Related Concept Videos
Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Conserved 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...
Conservation 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...
Conservation 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...
Protein 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.
Nucleic Acid Structure
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
DNA Structure
DNA has a double-helix structure. The...

