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Protein Organization

Protein Organization

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

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

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Protein Folding

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...

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Related Experiment Video

Updated: May 10, 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 threading using context-specific alignment potential.

Jianzhu Ma¹, Sheng Wang, Feng Zhao

¹Toyota Technological Institute at Chicago, IL 60637, USA.

Bioinformatics (Oxford, England)

|July 2, 2013

Summary

This summary is machine-generated.

We developed a new context-specific alignment potential to improve protein threading accuracy. This method enhances alignment and template selection, particularly for distantly related proteins, overcoming key limitations in 3D structure prediction.

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Science

Background:

Template-based modeling, including homology modeling and protein threading, is crucial for protein 3D structure prediction.
Alignment errors and suboptimal template selection remain significant challenges, especially for distantly related proteins.

Purpose of the Study:

To introduce a novel context-specific alignment potential for protein threading.
To enhance the accuracy of alignment and template selection in protein structure prediction.

Main Methods:

Developed a context-specific alignment potential integrating local and global information.
Quantified alignment quality using log-odds ratios based on context-specific residue and positional information.
Incorporated correlations among protein features and utilized context-specific, structural, and global data.

Main Results:

The novel alignment potential significantly outperforms existing context-independent and profile-based scoring functions.
Demonstrated superior alignment and threading results on large benchmarks compared to state-of-the-art profile-based methods.
Showcased particular effectiveness for distantly related proteins and those with sparse sequence profiles.

Conclusions:

The proposed context-specific alignment potential offers a more sensitive and accurate approach to protein threading.
This method effectively addresses the limitations of current template-based modeling, especially for challenging protein targets.
Improved protein 3D structure prediction capabilities, particularly for evolutionary distant proteins.