Related Experiment Video
Updated: Aug 18, 2026

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
A comprehensive and non-redundant database of protein domain movements
Guoying Qi1, Richard Lee, Steven Hayward
1School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
Motivation:
The current DynDom database of protein domain motions is a user-created database that suffers from selectivity and redundancy. The aim of the analysis presented here was to overcome both these limitations and to produce both a comprehensive and a non-redundant description of domain movements from structures stored in the current protein data bank.
Results:
A multi-step procedure is applied that starts with grouping proteins in the structural databank into families based on sequence similarity. Multiple sequence alignment, conformational clustering and a dimensional clustering method based on the Gram-Schmidt algorithm are applied to members of each family to remove dynamic redundancy in their domain movements. Representative domain movements are described in terms of domains, hinge axes and hinge-bending residues using the DynDom program. The results show that within an average family of 11.5 members, there are on average only 1.31 different domain movements indicating a high redundancy in the movements these structures represent. This verifies earlier findings that domain movements are usually highly controlled. Despite the removal of this considerable redundancy, the process has resulted in double the number of domain movements stored in the user-created database. The data are organized in a relational database with a web-interface.
Availability:
The database can be browsed and searched at http://www.cmp.uea.ac.uk/dyndom
Contact:
sjh@cmp.uea.ac.uk.
More Related Videos
Related Concept Videos
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...
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...
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...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

