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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: Jun 26, 2026

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Published on: December 9, 2016

Stabbing balls and simplifying proteins.

Ovidiu Daescu¹, Jun Luo

¹Department of Computer Science, University of Texas at Dallas, MS-EC 31, Richardson, TX 75080, USA. daescu@utdallas.edu

International Journal of Bioinformatics Research and Applications

|January 13, 2009

Summary

This summary is machine-generated.

This study introduces an algorithm to simplify molecule chains by minimizing stabbing points for indexed balls, crucial for protein data visualization and searching. Experiments show significant simplification ratios on protein databases.

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Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Area of Science:

Computational geometry
Bioinformatics
Structural biology

Background:

Protein chains are complex structures requiring simplification for efficient analysis and visualization.
Existing methods may not optimally reduce complexity for applications like database searching.

Purpose of the Study:

To develop and implement an algorithm for simplifying sequences of indexed balls (representing molecular structures).
To minimize the number of stabbing points (m) required to represent the chain, where each segment connects two points and stabs intermediate balls.

Main Methods:

Formulated the problem as finding a minimal sequence of stabbing points for indexed balls in 3D space.
Implemented the algorithm and developed a web server accepting Protein Data Bank (PDB) files.
Conducted experiments on thousands of proteins from the PDB Bank.

Main Results:

The algorithm successfully simplifies protein chains by reducing the number of segments needed for representation.
Experimental validation on a large dataset of proteins demonstrated notable simplification ratios.
A web server was created for practical application of the simplification algorithm.

Conclusions:

The developed algorithm provides an effective method for simplifying molecular chains, particularly proteins.
This simplification aids in visualization, matching, and efficient searching within molecular and protein databases.
The approach offers a quantifiable measure of simplification through experimental validation on extensive datasets.