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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 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 and Protein Structures

Protein and Protein Structures

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 Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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...

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Updated: May 20, 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

Template-based protein structure modeling using the RaptorX web server.

Morten Källberg¹, Haipeng Wang, Sheng Wang

¹Toyota Technological Institute at Chicago, Chicago, Illinois, USA.

Nature Protocols

|July 21, 2012

Summary

Understanding protein function requires accurate 3D atomic models. The RaptorX web server provides reliable protein structure prediction, even with distant templates, aiding biological research.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Determining the functional roles of proteins is essential in modern biology.
Reliable three-dimensional (3D) atomic models of proteins are crucial for understanding their function.
The proteome comprises numerous protein entities, many with unknown functions.

Purpose of the Study:

To present a community-wide, web-based method for protein structure prediction using RaptorX.
To improve protein secondary structure prediction, template-based tertiary structure modeling, and alignment quality assessment.
To enhance the accuracy of alignments between target sequences and distantly related template proteins.

Main Methods:

Utilizing the RaptorX web server for protein structure prediction.
Employing sophisticated probabilistic alignment sampling.
Implementing a novel nonlinear scoring function and a probabilistic-consistency algorithm.
Assessing alignment quality for template-based modeling.

Main Results:

RaptorX delivers high-quality structural models, particularly for targets with only remote templates.
The server excels in aligning target sequences with distantly related template proteins, even with sparse sequence profiles.
The method incorporates advanced alignment techniques, including probabilistic sampling and a nonlinear scoring function.

Conclusions:

RaptorX provides a valuable tool for predicting protein structures, facilitating the study of protein function.
The web server's advanced algorithms enable accurate modeling even when template information is limited.
RaptorX has been widely adopted, processing thousands of sequences since its release.