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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
A database of domain definitions for proteins with complex interdomain geometry
Indraneel Majumdar1, Lisa N Kinch, Nick V Grishin
1Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America. indraneel@chop.swmed.edu
Plos One
|April 9, 2009
Summary
This study introduces a new database of manually defined protein structural domains, offering unique insights into protein evolution and folding. These refined domain definitions aid in analyzing proteins often left undivided by existing databases.
Area of Science:
- Structural biology
- Bioinformatics
- Evolutionary biology
Background:
- Protein structural domains are crucial for understanding protein folding and evolution.
- Existing databases struggle with defining domains and their boundaries for certain proteins.
- Manual domain definition is challenging but necessary for a comprehensive understanding.
Purpose of the Study:
- To present a novel database of manually defined structural domains for multi-domain proteins.
- To provide refined domain definitions, including residue boundaries, for proteins not split by existing databases.
- To offer a resource for studying protein domain properties and evolution.
Main Methods:
- Manual definition of structural domains for a representative set of proteins from the SCOP multi-domain class.
- Consideration of domains as mobile evolutionary and independently folding units.
- Refinement of alternate domain definitions using structural similarity, functional sites, and automated methods.
Main Results:
- A novel database of manually defined structural domains is presented (http://prodata.swmed.edu/multidom/).
- Alternate domain definitions were retained and refined, addressing limitations in existing databases.
- The database includes residue boundaries for proteins typically not delineated by SCOP and CATH.
Conclusions:
- The database provides valuable, refined domain definitions for proteins, aiding evolutionary and folding studies.
- These definitions are suitable for sequence and structure searches and for training domain delineation algorithms.
- The resource facilitates a deeper understanding of protein domain properties and evolutionary dynamics.
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