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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 Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein and Protein Structure02:15

Protein and Protein Structure

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...
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...

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Related Experiment Video

Updated: May 19, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy

Debswapna Bhattacharya1, Jianlin Cheng

  • 1Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA.

Proteins
|August 29, 2012
PubMed
Summary
This summary is machine-generated.

Computational protein structure prediction models often deviate from native structures. Our 3Drefine protocol consistently improves these models using hydrogen bonding optimization and energy minimization, aiding drug design.

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Last Updated: May 19, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biochemistry

Background:

  • Computational protein structure prediction accuracy is limited by deviations from native structures.
  • These deviations hinder applications in drug design and biochemical analysis.
  • Protein structure refinement remains a significant challenge, with most methods failing to consistently improve model quality.

Purpose of the Study:

  • To develop a robust and computationally inexpensive protocol for refining predicted protein structures.
  • To improve the accuracy of computational protein structure prediction models for downstream applications.

Main Methods:

  • A two-step refinement protocol, 3Drefine, was developed.
  • Step 1: Optimization of the hydrogen bonding (HB) network.
  • Step 2: Atomic-level energy minimization using composite physics and knowledge-based force fields.

Main Results:

  • 3Drefine consistently improved both global and local structural quality measures on CASP benchmark data.
  • The method demonstrated significant improvements over initial predicted structures.
  • The protocol is computationally inexpensive, requiring only minutes of CPU time for typical protein lengths.

Conclusions:

  • 3Drefine offers a consistent and effective solution for protein structure refinement.
  • The protocol enhances the utility of computational protein structure prediction for drug design and biochemical studies.
  • A freely available web server facilitates access to the 3Drefine method.