Thermodynamics of Enzyme-Catalyzed Reactions
| Enzyme | Thermodynamics of Enzyme-Catalyzed Reactions | NIST |
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Thermodynamics of Enzyme-Catalyzed Reactions |
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In citing this work please use:
Goldberg RN, Tewari YB, Bhat TN, "Thermodynamics of
Enzyme-Catalyzed Reactions -a Database for Quantitative
Biochemistry", Bioinformatics 2004;20(16):2874-2877.
DOWN LOADS
| Mathematica Article | 1.Yes | |
| BioEqCalc.m |
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A computer package “BioEqCalc” for treating complex equilibria in aqueous solutions has been developed.1 The package is geared towards the treatment of biochemical systems and as such yields information on the molalities and mole fractions of the species in the solution, the activity coefficients of the species and the activity of the solvent (H2O), values of apparent equilibrium constants K', standard transformed Gibbs free energies DrG'° and standard transformed enthalpies of reaction DrH'°, calorimetric enthalpies of reaction DrH(cal), and changes in the binding DrN(X) of ligands such as X = H+ and Mg2+. Constraints such as constant pH, pX, and ionic strength I can be introduced into the calculations. The effects of ionic strength are accounted for in the computation. The chemical equilibrium problem is defined by input of the data in a convenient chemical format. Two and three dimensional plots of the apparent equilibrium constant as a function of temperature, pX, and ionic strength can be produced.
These codes are written in Mathematica2 and can be downloaded from this web-site( see above). These codes are: “Article.nb” and “BioEqCalc.m”. Note that the extensions must be kept as “.nb” and “.m” for the codes to work. Also, in “Article.nb”, the first executable step is to load the “BioEqCalc.m” package. Thus where it says “The initial step is to load the BioEqCalc package,” one must give the correct path to “BioEqCalc.m”.
1D. L. Akers and R. N. Goldberg; "BioEqCalc: A package for performing equilibrium calculations on biochemical reactions," Mathematica J., 8, 86-113 (2001).
2Certain commercial software are identified in this web-site. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology (NIST), nor is it intended to imply that the software identified are necessarily the best available for the purpose.