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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

Protein Organization

Protein and Protein Structure

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...

Protein Folding

Protein Folding

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Related Experiment Video

Updated: Jun 12, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein structure determination via an efficient geometric build-up algorithm.

Robert T Davis¹, Claus Ernst, Di Wu

¹Department of Mathematics and Computer Science, Bioinformatics and Information Sciences Center, Western Kentucky University, Bowling Green, KY 42103, USA.

BMC Structural Biology

|May 22, 2010

Summary

This summary is machine-generated.

A new Revised Updated Geometric Build-up (RUGB) algorithm improves protein structure determination from sparse distance data. This revised algorithm is more efficient and reduces numerical errors compared to the previous UGB method.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational biology
Structural bioinformatics
Biophysics

Background:

Protein structure determination relies on solving distance geometry problems using inter-atomic distances.
The general distance geometry problem is NP-hard, posing computational challenges.
The Updated Geometric Build-up (UGB) algorithm was developed for protein structure determination with sparse distance data, controlling numerical errors.

Purpose of the Study:

To improve the efficiency and effectiveness of solving distance geometry problems for protein structure determination.
To present a revised algorithm that addresses limitations of the UGB method.

Main Methods:

Developed the Revised Updated Geometric Build-up (RUGB) algorithm.
Relaxed the iterative condition for determining unpositioned atoms compared to the UGB algorithm.
Incorporated data structure techniques to enhance algorithmic efficiency and effectiveness.

Main Results:

The RUGB algorithm demonstrated smaller numerical errors than the UGB algorithm.
The RUGB algorithm achieved a significantly reduced runtime compared to the UGB algorithm.
Testing was conducted on randomly selected proteins from the Protein Structure Database (PDB).

Conclusions:

The RUGB algorithm enhances protein structure determination by relaxing update conditions and using efficient data structures.
Key improvements include a reduction in overall runtime and a decrease in numerical error.
The RUGB algorithm offers a more effective approach for determining protein structures from sparse exact distance data.