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Related Concept Videos

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,...
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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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Related Experiment Video

Updated: May 16, 2026

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes
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2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Published on: August 6, 2018

NPIDB: Nucleic acid-Protein Interaction DataBase.

Dmitry D Kirsanov1, Olga N Zanegina, Evgeniy A Aksianov

  • 1Department of Mathematical Methods in Biology, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

Nucleic Acids Research
|November 30, 2012
PubMed
Summary

The Nucleic acid-Protein Interaction DataBase offers updated structural data for DNA-protein and RNA-protein complexes. This resource aids in understanding nucleoprotein interactions through enhanced tools and classifications.

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

Published on: March 3, 2015

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Last Updated: May 16, 2026

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes
08:23

2 in 1: One-step Affinity Purification for the Parallel Analysis of Protein-Protein and Protein-Metabolite Complexes

Published on: August 6, 2018

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

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

Published on: March 3, 2015

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biochemistry

Background:

  • Nucleic acid-protein interactions are fundamental to cellular processes.
  • The Protein Data Bank (PDB) is a primary source for structural data of these complexes.
  • Previous versions of the database have provided valuable insights.

Purpose of the Study:

  • To present an upgraded version of the Nucleic acid-Protein Interaction DataBase (NPIDB).
  • To enhance the understanding of DNA-protein and RNA-protein complexes.
  • To provide researchers with advanced tools for analyzing nucleoprotein interactions.

Main Methods:

  • Data extraction from the Protein Data Bank (PDB).
  • Development of a new web interface for NPIDB.
  • Implementation of new tools for calculating intermolecular interactions.
  • Classification of SCOP families relevant to DNA-binding domains.
  • Inclusion of data on conserved water molecules at the DNA-protein interface.

Main Results:

  • NPIDB now contains information on 3846 DNA-protein and RNA-protein complexes (as of October 2012).
  • The database features a user-friendly web interface and specialized analysis tools.
  • Weekly updates ensure the content is current.
  • New features include SCOP family classification and conserved water molecule data.

Conclusions:

  • The upgraded NPIDB provides a comprehensive and continuously updated resource for studying nucleoprotein complexes.
  • Enhanced tools and data facilitate deeper biological interpretation of structural information.
  • This database is a valuable asset for researchers in structural biology, bioinformatics, and molecular biology.