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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

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...
Membrane Domains01:18

Membrane Domains

The membrane domains concentrate specific lipids and proteins at one place within the membrane, which helps in cell signaling, adhesion, and other critical cellular processes. These domains can differ in size, composition, function, and lifespan.
Protein Domains
The membrane comprises a group of distinct proteins responsible for carrying out a cell's specific function. For example, the plasma membrane of the human sperm, or a single germ cell, contains a unique set of proteins in the anterior...
Conservation of Protein Domains02:26

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...
Mechanisms of Membrane Domain Formation00:59

Mechanisms of Membrane Domain Formation

Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with cytoskeletal...
Three-Domain System of Life01:21

Three-Domain System of Life

Ribosomal RNA (rRNA) sequence analysis revealed three distinct groups of cells: eukaryotes, bacteria, and archaea. In 1978, Carl R. Woese proposed the concept of domains, a taxonomic level above kingdoms, to differentiate these groups. He suggested that archaea and bacteria, despite their similar appearance, represent separate domains. Domains differ in rRNA, membrane lipid structure, transfer RNA, and antibiotic sensitivity.In this classification, animals, plants, and fungi belong to the...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

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Related Experiment Video

Updated: Jul 15, 2026

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile.

Hongyi Zhou1, Bin Xue, Yaoqi Zhou

  • 1Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.

Protein Science : a Publication of the Protein Society
|April 26, 2007
PubMed
Summary

We developed DDOMAIN, a new method for protein domain division, achieving high consistency with author annotations. DDOMAIN offers accurate protein structural and functional characterization by identifying protein domains.

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Last Updated: Jul 15, 2026

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
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Published on: October 3, 2018

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Mapping Dysfunctional Protein-Protein Interactions in Disease

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate protein domain division is crucial for understanding protein structure and function.
  • Existing methods for domain annotation vary in accuracy and consistency.

Purpose of the Study:

  • To develop and evaluate DDOMAIN, a novel computational method for automatic protein domain division.
  • To compare DDOMAIN's performance against established domain annotation databases and methods.

Main Methods:

  • DDOMAIN utilizes a normalized contact-based domain-domain interaction profile for structure division.
  • Performance was assessed by comparing DDOMAIN's output with author annotations, SCOPe, and CATH databases.
  • Adjustable parameters in DDOMAIN were trained using author annotations for optimal performance.

Main Results:

  • DDOMAIN demonstrated high agreement with author annotations (90% in domain count, 88% in residue overlap).
  • Trained DDOMAIN showed superior consistency with SCOPe and CATH compared to other automatic methods like PDP and DomainParser 2.
  • Performance remained robust across proteins with varying domain numbers, including multi-domain proteins.

Conclusions:

  • DDOMAIN provides a reliable and accurate method for automatic protein domain division.
  • The method shows significant consistency with expert and author-defined domain boundaries.
  • DDOMAIN advances the field of protein structural and functional characterization through improved domain annotation.