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The Hilser Lab - Johns Hopkins University

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117A Mudd Hall
Department of Biology
Johns Hopkins University
3400 N. Charles Street
Baltimore, MD 21218-2685


Email: hilser@jhu.edu
Office 410 516-6072
Lab 410 516-6757
Departmental fax 410 516-5213

 

COREX / BEST

The COREX algorithm reconstructs a protein's sequence-specific energy profile from a high-resolution structure. It was originally developed to capture the hydrogen exchange behavior that is observed for proteins under native conditions. The hallmark feature of the COREX approach is that rather than treating proteins as single conformations, which structurally evolve over a time course, COREX generates an instantaneous ensemble. The current version of this algorithm, significantly enhanced since its original publication in 1996, is referred to as COREX/BEST or simply BEST (Biology using Ensemble-based Structural Thermodynamics).

Please cite usage of COREX/BEST web-interface results with: Vertrees J., Barritt P., Whitten S., and V. J. Hilser. COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures. (2005) Bioinformatics. 21: 3318-3319.

Please cite usage of the COREX/BEST algorithm with the following two papers: [Hilser, V. J., & Freire, E. (1996). Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. Journal of molecular biology, 262(5), 756-772.] and [Hilser, V. J., García-Moreno E, B., Oas, T. G., Kapp, G., & Whitten, S. T. (2006). A statistical thermodynamic model of the protein ensemble. Chemical reviews, 106(5), 1545-1558.]


eScape Portal

eScape (Energetic landScape) is a sequence-based algorithm that reconstructs a protein's stability profile using thermodynamic information calculated from a protein's primary sequence information.

Please cite your usage of eScape with the following two publications: [Gu, J., & Hilser, V. J. (2008). Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome. Structure, 16(11), 1627-1637.] and [Gu, J., & Hilser, V. J. (2009). Sequence-based analysis of protein energy landscapes reveals nonuniform thermal adaptation within the proteome. Molecular biology and evolution, 26(10), 2217-2227.]


HePCaT Portal

The Horizontal Protein Comparison Tool (HePCaT) is a generalized alignment tool that returns the optimal pairwise gapped alignment between multiple arbitrary sets of signed numerical values. The HePCaT algorithm provides an objective data mining method for the detection and comparison of numerical trends in various protein or nucleic acid data, such as hydropathy, positional thermodynamic stability, and mRNA translation efficiency. The algorithm’s flexible comparison engine (based on both relative shape and absolute similarity measures) does not rely on explicit gap penalties, and includes an empirical probability model to estimate the statistical significance of the returned alignment.

Please cite your usage of HePCaT with: Hadzipasic, O., Wrabl J.O., Hilser, V.J. (2013). A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy. PLoS Comp. Biol. 9(10), e1003247.