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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging.

Vahid Mirjalili¹, Keenan Noyes, Michael Feig

¹Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan, 48824; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824.

|June 6, 2013

Summary

This summary is machine-generated.

Molecular dynamics simulations refined protein structures for the CASP10 competition. Selecting and averaging structures from molecular dynamics ensembles improved protein structure prediction accuracy.

Keywords:

CASP protein quality assessment scoring structure prediction

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Last Updated: May 10, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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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

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Protein structure prediction is crucial for understanding biological function.
The Critical Assessment of Techniques for Protein Structure Prediction (CASP) benchmarks prediction methods.
Molecular dynamics (MD) simulations offer a powerful approach for refining protein models.

Purpose of the Study:

To evaluate the performance of MD simulations for protein structure refinement in CASP10.
To analyze key factors influencing the success of MD-based refinement.
To provide insights into optimizing MD simulation strategies for protein structure prediction.

Main Methods:

Utilized molecular dynamics (MD) simulations for structure refinement of CASP10 targets.
Employed ensemble selection and structural averaging from MD trajectories.
Investigated the impact of various restraint types and sampling strategies (multiple short vs. single long simulations).

Main Results:

The MD-based refinement method demonstrated overall performance in CASP10.
A quality assessment criterion proved successful in selecting accurate structures.
Analysis revealed the impact of scoring versus averaging and a final refinement step.

Conclusions:

MD simulations, combined with ensemble selection and averaging, are effective for protein structure refinement.
Careful consideration of restraint types, sampling, and quality assessment is vital for optimal performance.
The study provides valuable insights for improving computational protein structure prediction techniques.