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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 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 Organization

Protein Organization

Structural Protein Function

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...

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Updated: May 22, 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

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.

Ambrish Roy¹, Jianyi Yang, Yang Zhang

¹Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA.

Nucleic Acids Research

|May 10, 2012

Summary

This summary is machine-generated.

We created COFACTOR, a webserver for protein function annotation using 3D structures. It outperforms sequence-based methods for predicting protein-ligand binding sites and enzyme functions.

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Area of Science:

Structural bioinformatics
Computational biology
Protein function prediction

Background:

Accurate protein function annotation is crucial for biological research.
Traditional sequence-based methods have limitations in predicting complex functions.
Structure-based approaches offer complementary insights into protein function.

Purpose of the Study:

To develop an automated webserver, COFACTOR, for structure-based protein function annotation.
To predict protein-ligand binding interactions, Enzyme Commission numbers, and Gene Ontology terms from protein structures.
To provide a user-friendly platform for researchers to annotate protein functions.

Main Methods:

COFACTOR utilizes structure threading through template libraries of known protein-ligand interactions, EC numbers, and GO terms.
It combines global and local structural similarity scoring for confidence evaluation.
The webserver is benchmarked against large-scale datasets and compared with sequence-based methods.

Main Results:

COFACTOR demonstrates significant advantages over traditional sequence-based annotation methods.
It achieved top performance in protein-ligand binding site prediction during the CASP9 experiment.
The webserver provides reliable functional insights based on structural templates.

Conclusions:

COFACTOR is an effective automated tool for structure-based protein function annotation.
It enhances the prediction accuracy of protein-ligand binding sites and functional annotations.
The freely available webserver facilitates biological discovery.