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Related Concept Videos

Protein Organization01:24

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....
9.7K

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PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

Lim Heo1, Michael Feig1

  • 1Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.

Bioinformatics (Oxford, England)
|November 11, 2017
PubMed
Summary
This summary is machine-generated.

The PREFMD web server refines protein structure models using molecular dynamics. It offers improved global accuracy compared to other methods, aiding structural bioinformatics research.

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Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Biophysics

Background:

  • Protein structure model refinement is a critical challenge in structural bioinformatics.
  • Molecular dynamics (MD)-based approaches offer a promising strategy for consistent protein structure refinement.

Purpose of the Study:

  • To present the PREFMD web server, an optimized tool for protein structure refinement.
  • To evaluate the performance of PREFMD against state-of-the-art refinement servers.

Main Methods:

  • Implementation of an optimized molecular dynamics protocol based on a previously validated method.
  • Utilizing the PREFMD web server for automated protein structure refinement.
  • Validation against recent protein refinement targets from the Critical Assessment of protein Structure Prediction (CASP) competition.

Main Results:

  • PREFMD consistently improves global structure accuracy of protein models.
  • The server demonstrates more significant improvements compared to other leading refinement tools.
  • Validation results confirm the effectiveness of the optimized protocol.

Conclusions:

  • The PREFMD web server provides an effective and accessible solution for protein structure refinement.
  • The optimized molecular dynamics protocol enhances the accuracy of protein structure models.
  • PREFMD represents a valuable resource for the structural bioinformatics community.