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von Bertalanffy
An algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential. This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source.
SSTMap / Solvation Structure and Thermodynamic Mapping
Maps out measures of water structure and thermodynamics on solute surfaces. SSTMap is a computational tool that combines thermodynamic analysis with structural analysis, which can aid in understanding and evaluating the displacement of active-site water molecules. The software provides access to individual functions, such as identification of hydration site clusters, calculation of voxel occupancies, energy, entropy, and hydrogen bonding calculations.
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