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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...
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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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,...

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Related Experiment Video

Updated: May 8, 2026

Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Predicting protein-DNA interactions by full search computational docking.

Victoria A Roberts1, Michael E Pique, Lynn F Ten Eyck

  • 1San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, 92093.

Proteins
|August 23, 2013
PubMed
Summary
This summary is machine-generated.

Computational docking accurately predicts protein-DNA interactions, revealing binding sites and mechanisms. This method aids in understanding biological processes and designing new experiments when crystallography is challenging.

Keywords:
HIV integrasePoisson-Boltzmann electrostaticshydrogen/deuterium exchangelinker histoneprotein-DNA structuretranscription factoruracil-DNA glycosylase

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

Published on: January 26, 2024

Area of Science:

  • Structural Biology
  • Computational Biology
  • Molecular Interactions

Background:

  • Protein-DNA interactions are crucial for biological processes.
  • X-ray crystallography is limited by difficulties in crystallizing protein-DNA complexes and small DNA fragments.

Purpose of the Study:

  • To evaluate the computational program DOT for predicting protein-DNA interactions.
  • To compare docking results with experimental data for diverse protein-DNA systems.

Main Methods:

  • Utilized the DOT program for exhaustive, rigid-body docking of protein-DNA complexes.
  • Investigated four distinct protein-DNA interactions using computational methods.

Main Results:

  • Computational docking results strongly supported subsequent experimental findings for all four systems.
  • Identified mechanisms for DNA binding, large DNA-binding footprints, and multiple DNA contacts.
  • Docking predictions guided experimental design for uracil-DNA glycosylase (UNG).

Conclusions:

  • DOT's electrostatic energy effectively represents DNA and protein electrostatic properties.
  • Computational docking can identify protein-DNA interactions and expand structural understanding beyond crystallographic data.
  • This method aids in understanding biological mechanisms and experimental design.