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Protein Organization

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 Organization

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
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Protein and Protein Structure

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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.
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Related Experiment Video

Updated: Mar 21, 2026

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

3Drefine: an interactive web server for efficient protein structure refinement.

Debswapna Bhattacharya¹, Jackson Nowotny¹, Renzhi Cao¹

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

Nucleic Acids Research

|May 1, 2016

Summary

This summary is machine-generated.

3Drefine offers efficient protein structure refinement and analysis via an interactive web server. This tool improves both global and local structural quality, providing valuable insights for researchers.

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Last Updated: Mar 21, 2026

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Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

Protein structure refinement is crucial for understanding biological function.
Accurate protein models are essential for drug discovery and molecular biology research.
Existing refinement methods may lack efficiency or comprehensive analysis capabilities.

Purpose of the Study:

To develop and present 3Drefine, an interactive web server for efficient protein structure refinement.
To provide integrated tools for statistical and visual analysis of refined protein models.
To enhance the accessibility and usability of protein structure refinement tools for the scientific community.

Main Methods:

Utilizes iterative optimization of hydrogen bonding networks.
Employs atomic-level energy minimization with composite physics and knowledge-based force fields.
Evaluated using blind CASP experiments and large-scale benchmark datasets.

Main Results:

Demonstrates consistent improvement in global and local structural quality measures compared to initial structures.
Provides web-based statistical feedback and interactive visualization of refined models using JSmol.
Successfully validated through extensive testing on diverse datasets and CASP experiments.

Conclusions:

3Drefine offers a computationally efficient and user-friendly platform for protein structure refinement.
The server integrates refinement with comprehensive analysis tools, enhancing its utility.
3Drefine is freely accessible, providing a valuable resource for researchers in structural biology and bioinformatics.