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Extracting representative structures from protein conformational ensembles.

Alberto Perez1, Arijit Roy, Koushik Kasavajhala

  • 1Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.

Proteins
|July 1, 2014
PubMed
Summary
This summary is machine-generated.

Selecting a single representative structure from biomolecular conformational ensembles can be misleading. New, inexpensive averaging methods offer superior representations for comparison with experimental data.

Keywords:
CASPaveragingclusteringensemblesmolecular dynamicsproteinroot mean square deviation

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Area of Science:

  • Computational biology
  • Structural biology
  • Biophysics

Background:

  • Numerous computational methods generate conformational ensembles for biomolecules.
  • Typically, a single structure is chosen to represent the entire ensemble, often the one closest to the center of the largest cluster.
  • This common practice may not yield the most accurate representation of the ensemble's average structure.

Purpose of the Study:

  • To address the limitations of selecting single representative structures from conformational ensembles.
  • To introduce computationally inexpensive protocols for generating improved representations of biomolecular systems.
  • To facilitate more direct comparisons between computational models and experimental data, such as X-ray crystallography.

Main Methods:

  • Development and application of two novel, computationally inexpensive averaging protocols.
  • Analysis of conformational ensembles generated by various biomolecular simulation methods.
  • Comparison of structures generated by averaging protocols with conventionally selected representative structures.

Main Results:

  • The conventionally selected representative structure is not always the best representation of a cluster.
  • The proposed averaging protocols systematically provide better representations of conformational ensembles.
  • These improved representations allow for more accurate comparisons with experimental structures.

Conclusions:

  • Averaging protocols offer a more robust method for representing biomolecular conformational ensembles than single-structure selection.
  • The developed methods are computationally inexpensive and enhance the utility of simulation data.
  • Systematic errors within the generated ensembles can ultimately limit the achievable accuracy of any representation method.