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COREX/BEST server: a web browser-based program that calculates regional stability variations within protein

Jason Vertrees1, Phillip Barritt, Steve Whitten

  • 1Department of Human Biological Chemistry & Genetics, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.

Bioinformatics (Oxford, England)
|June 1, 2005
PubMed
Summary
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The COREX/BEST Server analyzes protein structures to predict regional stability variations. This tool generates a conformational ensemble, offering insights into protein thermodynamics and stability at the residue level.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • The COREX/BEST Server is accessible via web browser at http://best.utmb.edu/BEST/.
  • It provides a user-friendly interface for analyzing protein structures.

Purpose of the Study:

  • To introduce the COREX/BEST Server for generating protein structural thermodynamic ensembles.
  • To enable calculation and visualization of regional protein stability variations.

Main Methods:

  • Input user-provided protein structure coordinates.
  • Generate a conformational ensemble using the COREX/BEST algorithm.
  • Calculate regional stability variations at the residue level in kcal/mol.

Main Results:

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  • The server produces a structural thermodynamic ensemble from protein coordinates.
  • Regional stabilities are calculated and presented in energy units (kcal/mol).
  • Calculated stabilities can be mapped onto the protein structure for visualization and downloaded as tab-delimited text.

    • Conclusions:

    • The COREX/BEST Server facilitates the analysis of protein structural stability.
    • It offers a method for visualizing and quantifying regional stability variations.
    • The server provides accessible theoretical and algorithmic information with references.