MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs
Related Experiment Video
Updated: Jul 10, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Hua Cheng1, Bong-Hyun Kim, Nick V Grishin
1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA.
Abstract:
We describe MALIDUP (manual alignments of duplicated domains), a database of 241 pairwise structure alignments for homologous domains originated by internal duplication within the same polypeptide chain. Since duplicated domains within a protein frequently diverge in function and thus in sequence, this would be the first database of structurally similar homologs that is not strongly biased by sequence or functional similarity. Our manual alignments in most cases agree with the automatic structural alignments generated by several commonly used programs. This carefully constructed database could be used in studies on protein evolution and as a reference for testing structure alignment programs. The database is available at http://prodata.swmed.edu/malidup.
More Related Videos
Related Concept Videos
Genome Annotation and Assembly
Conserved Binding Sites
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
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
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Organization
The primary structure of a protein is its amino acid sequence.
Nucleic Acid Structure
DNA Structure
DNA has a double-helix structure. The...

