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Updated: Nov 29, 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

Molecular-replacement phasing using predicted protein structures from AWSEM-Suite.

Shikai Jin^1,2, Mitchell D Miller², Mingchen Chen¹

¹Center for Theoretical Biological Physics, Rice University, Houston, Texas, USA.

|November 19, 2020

Summary

This summary is machine-generated.

The Associative memory, Water-mediated, Structure and Energy Model Suite (AWSEM-Suite) effectively predicts protein structures for molecular replacement when no solved template exists. AWSEM-Suite often outperforms other methods in solving the X-ray crystallography phase problem.

Keywords:

AWSEM-Suite molecular replacement structure prediction

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Area of Science:

Structural biology
X-ray crystallography
Computational biology

Background:

The X-ray crystallography phase problem hinders structure determination by preventing direct measurement of wave phases.
Molecular replacement (MR) typically relies on solved template structures to estimate these phases.
Finding suitable templates is crucial, but challenging when sequence similarity is low.

Purpose of the Study:

To evaluate the effectiveness of AWSEM-Suite predicted structures for molecular replacement.
To determine if AWSEM-Suite can extend the applicability of MR to proteins with low sequence similarity to known structures.

Main Methods:

Utilized structures generated by the AWSEM-Suite prediction algorithm.
Assessed the performance of AWSEM-Suite in molecular replacement.
Compared AWSEM-Suite performance against I-TASSER-MR and AWSEM-Template.

Main Results:

AWSEM-Suite predicted structures proved effective for molecular replacement.
The algorithm successfully provided useful phase information, aiding structure determination.
AWSEM-Suite demonstrated superior performance compared to I-TASSER-MR and AWSEM-Template.

Conclusions:

AWSEM-Suite is a valuable tool for solving the phase problem in X-ray crystallography.
Predicted protein models can successfully facilitate molecular replacement, expanding its scope.
This approach enhances the ability to determine structures for proteins lacking homologous templates.