Using the COREX/BEST server to model the native-state ensemble

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. © 2014 Springer Science+Business Media,New York.