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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: 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

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local

Aram Davtyan¹, Nicholas P Schafer, Weihua Zheng

¹Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States.

The Journal of Physical Chemistry. B

|May 2, 2012

Summary

This summary is machine-generated.

The associative memory, water mediated, structure and energy model (AWSEM) aids protein structure prediction. By integrating sequence data, AWSEM improves predictions, especially when using homologous sequences for fragment selection.

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Area of Science:

Computational biology
Biophysics
Protein structure prediction

Background:

The Associative Memory, Water Mediated, Structure and Energy Model (AWSEM) is a coarse-grained protein force field.
It incorporates physically motivated terms like hydrogen bonding and bioinformatically derived local structure biasing.
AWSEM accounts for many-body effects influenced by local protein sequences.

Purpose of the Study:

To evaluate AWSEM's de novo protein structure prediction capabilities.
To assess prediction accuracy using different levels of global homology for local structure biasing.
To investigate the impact of homologous sequence information on prediction performance.

Main Methods:

Utilizing AWSEM with a local sequence alignment method based on short residue sequences (fragments).
Testing structure prediction across three homology levels between target and database sequences.
Comparing AWSEM predictions with and without homologous sequence information.

Main Results:

AWSEM predictions show modest improvements over related methods when no homologous sequences are available.
Including a few homologous sequences offers marginal prediction enhancement.
Restricting fragment search to homologous sequences enables high-resolution structure prediction.

Conclusions:

AWSEM is a viable tool for de novo protein structure prediction, particularly when guided by homologous sequence data.
The model's performance is sensitive to the selection of homologous sequences for fragment biasing.
AWSEM shows potential for future applications in protein kinetics and dynamics studies.