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Related Concept Videos

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...
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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,...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Mapping Dysfunctional Protein-Protein Interactions in Disease
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Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

The Protein-DNA Interface database.

Tomás Norambuena1, Francisco Melo

  • 1Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.

BMC Bioinformatics
|May 21, 2010
PubMed
Summary
This summary is machine-generated.

The Protein-DNA Interface database (PDIdb) provides structural data for 922 protein-DNA complexes. It aids research in molecular recognition, DNA binding protein design, and understanding transcription factor binding sites.

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

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Last Updated: Jun 12, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
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Published on: October 24, 2025

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Analyzing and Building Nucleic Acid Structures with 3DNA
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Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

  • Structural biology
  • Bioinformatics
  • Molecular biology

Background:

  • Protein-DNA interactions are crucial for biological processes.
  • Understanding these interactions requires detailed structural information.
  • Existing resources may not focus specifically on the atomic interface.

Purpose of the Study:

  • To create a curated database of protein-DNA complex structures.
  • To facilitate the study of molecular recognition rules between proteins and DNA.
  • To provide a resource for predicting DNA binding sites and designing novel proteins.

Main Methods:

  • Collected structural data from X-ray crystallography via the Protein Data Bank.
  • Developed a hierarchical functional classification (Class, Type, Subtype) for complexes.
  • Manually curated data using information from PDB, PubMed, CATH, SCOP, and COPS.
  • Included only structures with a resolution of 2.5 Å or higher.

Main Results:

  • The Protein-DNA Interface database (PDIdb) currently contains 922 entries.
  • Each entry represents a single, independent protein-DNA interface.
  • The database focuses on the atomic details of the interface, not just binding partners.

Conclusions:

  • PDIdb offers a valuable resource for researchers studying protein-DNA interactions.
  • The database supports advancements in predicting transcription factor binding sites.
  • It aids in the design of DNA-binding proteins with specific affinities and recognition properties.