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Protein Organization

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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....

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

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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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Updated: Sep 18, 2025

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

Artificial Intelligence (AI)-Based Protein Structure Prediction and Analysis.

Ashwani Kumar¹, Aanchal Gupta¹, Shubham Kumar¹

¹University Institute of Biotechnology, Chandigarh University, Gharuan Mohali, Punjab, India.

Methods in Molecular Biology (Clifton, N.J.)

|June 24, 2025

Summary

This summary is machine-generated.

Accurately predicting protein 3-D structures, especially using template-free methods, remains a major challenge in bioinformatics and drug discovery. Advanced artificial intelligence (AI) is crucial for overcoming computational complexity and improving protein structure prediction.

Keywords:

Artificial intelligence Bioinformatics Deep learning Protein structural prediction Search optimization

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

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Published on: July 25, 2013

Area of Science:

Computational Biology
Bioinformatics
Drug Discovery

Background:

Protein structure prediction is computationally complex, hindering drug design.
Template-based and template-free methods exist, but precise prediction for complex proteins remains difficult.
Ab initio prediction from amino acid sequences is an unresolved challenge.

Purpose of the Study:

To provide a comprehensive overview of template-free protein structure prediction research.
To discuss essential concepts, computational methods, and challenges in the field.
To offer insights and suggest future research directions for advancing computational protein structure prediction.

Main Methods:

Review of existing literature on template-free protein structure prediction.
Analysis of computational methods and their limitations.
Discussion of artificial intelligence (AI) approaches for protein structure prediction.

Main Results:

Template-free prediction is critical due to the increasing number of proteins with unknown structures.
AI methods show promise but face challenges related to complexity and resource limitations.
Current methods struggle with accurate prediction for complex protein structures.

Conclusions:

Sophisticated AI methods are essential for progress in protein structure prediction.
Further research is needed to overcome computational hurdles and resource limitations.
Advancing template-free prediction is key for effective drug discovery and bioinformatics.