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Using the COREX/BEST Server to Model the Native-State Ensemble

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Protein Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1084))

Abstract

Protein structures under normal conditions exist as ensembles of interconverting, transient microstates. A computer algorithm known as COREX/BEST (Biology using Ensemble-based Structural Thermodynamics) was developed to model microstate structures and describe the native ensembles of proteins in statistical thermodynamic terms. This algorithm has been tested extensively and validated through experimental comparisons examining a range of biophysical and functional phenomena, such as structural cooperativity, pH-dependent stability, and cold denaturation. Here, we describe a Web-based implementation of the COREX/BEST algorithm, called the COREX/BEST Server, and demonstrate how to use this online resource to characterize the structural and thermodynamic properties of the native protein ensemble.

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Acknowledgments

This work was supported by NIH grant R01-GM63747 to V.J.H. and the Texas Higher Education Coordinating Board grant 003615-0003-2011 to S.T.W.

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Authors and Affiliations

  1. Departments of Biology and Biophysics, Johns Hopkins University, Baltimore, MD, USA

    Vincent J. Hilser

  2. Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA

    Steven T. Whitten

Authors
  1. Vincent J. Hilser
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  2. Steven T. Whitten
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Editor information

Editors and Affiliations

  1. Department of Bioinformatics and Genomic, University of North Carolina at Charlott, Charlotte, North Carolina, USA

    Dennis R. Livesay

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Hilser, V.J., Whitten, S.T. (2014). Using the COREX/BEST Server to Model the Native-State Ensemble. In: Livesay, D. (eds) Protein Dynamics. Methods in Molecular Biology, vol 1084. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-658-0_14

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  • DOI: https://doi.org/10.1007/978-1-62703-658-0_14

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-657-3

  • Online ISBN: 978-1-62703-658-0

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