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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.
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Updated: Dec 21, 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

Protein Structure Prediction in CASP13 Using AWSEM-Suite.

Shikai Jin, Mingchen Chen, Xun Chen¹

¹Department of Chemistry, Rice University, Houston, Texas 77005, United States.

Journal of Chemical Theory and Computation

|May 13, 2020

Summary

This summary is machine-generated.

AWSEM-Suite improves protein structure prediction by combining template modeling and coevolutionary data with a physics-based force field. This approach enhances accuracy, especially for challenging targets, and enables functional studies.

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Published on: November 3, 2011

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

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

Published on: July 25, 2013

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

Protein tertiary structure prediction is crucial for understanding protein function.
Recent advancements include template-based modeling and coevolutionary restraints.
AWSEM-Suite integrates these techniques with a coarse-grained force field.

Purpose of the Study:

To evaluate the performance of the AWSEM-Suite algorithm in protein tertiary structure prediction.
To analyze the impact of template guidance and coevolutionary restraints on prediction accuracy.
To explore the suitability of AWSEM-Suite for functional investigations.

Main Methods:

AWSEM-Suite utilizes template-based modeling and coevolutionary restraints.
It incorporates a realistic coarse-grained force field (AWSEM) with optimized physical and bioinformatical energies.
The algorithm's performance was assessed in the CASP13 competition and through structure prediction tests on selected targets.

Main Results:

AWSEM-Suite demonstrated reliable predictions in CASP13, ranking eighth in free-modeling and hard-to-model categories.
High-resolution structure prediction was achieved, even with weak homology, by combining template and coevolutionary data.
Coevolutionary restraints sometimes decreased prediction quality for targets with reliable templates.

Conclusions:

AWSEM-Suite effectively uses template and coevolutionary information to guide protein structure prediction towards native-like states.
The algorithm's statistical mechanical basis and simulation capabilities allow for functional exploration beyond structure prediction.