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Related Concept Videos

Conserved Binding Sites01:49

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...
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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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 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...
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...

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Related Experiment Video

Updated: Jul 10, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

DIMA 2.0--predicted and known domain interactions.

Philipp Pagel1, Matthias Oesterheld, Oksana Tovstukhina

  • 1Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München, Am Forum 1, D-85350 Freising, Germany. p.pagel@wzw.tum.de

Nucleic Acids Research
|November 15, 2007
PubMed
Summary
This summary is machine-generated.

The Domain Interaction Map (DIMA) now integrates experimental and predicted domain-domain interactions, significantly enhancing genome and domain coverage for biological research.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jul 10, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Domain-domain interactions are crucial for understanding protein function and biological pathways.
  • Existing resources for domain interactions often lack comprehensive coverage or integration of diverse data types.

Purpose of the Study:

  • To enhance the Domain Interaction Map (DIMA) as an integrative resource for domain-domain interactions.
  • To improve coverage of genomes, domains, and prediction methodologies.

Main Methods:

  • Utilized SIMAP for exhaustive domain phylogenetic profiling across 460 genomes, covering 7038 Pfam domains.
  • Applied domain pair exclusion algorithms to experimental protein-protein interactions from IntAct (83,969 interactions) and predicted interactions from STRING.
  • Integrated experimental data from iPfam and 3did databases, identifying domain contacts in solved protein structures.

Main Results:

  • Achieved improved coverage of genomes and domains through domain phylogenetic profiling.
  • Generated 21,513 domain pairs with significant scores from experimental data and 2378 high-confidence pairs from predicted interactions.
  • Combined iPfam and 3did data to yield 3653 distinct interacting domain pairs.

Conclusions:

  • DIMA has evolved into a comprehensive resource by integrating multiple data sources and prediction algorithms.
  • The enhanced DIMA provides significantly improved coverage and insights into domain-domain interactions.
  • This resource facilitates deeper understanding of protein function and biological mechanisms.