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Related Concept Videos

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 Organization01:13

Protein Organization

Overview
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 Organization01:13

Protein Organization

Overview
Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Folding01:22

Protein Folding

Overview

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Related Experiment Video

Updated: Jun 28, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Voronoia: analyzing packing in protein structures.

Kristian Rother1, Peter Werner Hildebrand, Andrean Goede

  • 1International Institute for Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warszawa, Poland. krother@genesilico.pl

Nucleic Acids Research
|October 25, 2008
PubMed
Summary
This summary is machine-generated.

Voronoia is a new database providing atomic-scale packing data for protein structures. This data, including atomic volumes and packing densities, aids in understanding protein stability and function.

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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Related Experiment Videos

Last Updated: Jun 28, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Protein atom packing is crucial for stability and function.
  • Existing methods for analyzing protein packing have limitations.

Purpose of the Study:

  • To introduce Voronoia, a comprehensive database of atomic-scale packing data for protein 3D structures.
  • To provide tools for analyzing and visualizing protein packing characteristics.

Main Methods:

  • Developed an improved Voronoi Cell algorithm using hyperboloid interfaces.
  • Calculated atomic volumes, packing densities, and interior cavities for 61,318 protein structures from the PDB.
  • Integrated Jmol plugin for 3D visualization of packing data and cavities.

Main Results:

  • The Voronoia database contains detailed packing information for a large set of protein structures.
  • Analysis revealed comparisons of packing densities and cavities across SCOP superfamilies.
  • A web server and standalone version allow for on-demand calculations and visualization.

Conclusions:

  • Voronoia offers valuable atomic-scale packing data to enhance understanding of protein stability, function, and design.
  • The database and associated tools facilitate detailed structural analysis and visualization.
  • Accessible data and computational tools support diverse research applications in structural biology.