Back to stc main pageSTC performs free energy calculations from the structure of the different complexes in a graphical user interface. We have compiled executable versions for sgi, sun and linux PC which are accessible for free at the PENCE-MRC software download site.
In essence STC consists of two modules. The first module, calc_asa, calculates the change in accessible surface area (ASA) for the dissociation process from the coordinate files in the Brookhaven protein data bank (pdb) format using the algorithm ANAREA (Richmond, 1984) as implemented in the program VADAR (Wishart et al.,1994). The output files consists of the tabulated ASA of each atom of the complex, both the free forms of the enzyme and the ligand, as well the difference in ASA for each atom. The total changes in non-polar (all carbon atoms and sulfur atoms) and polar (all oxygen and nitrogen atoms) are summed up. In addition, the atomic change in ASA are regrouped per residues (and per side-chain) for calculating the change in S conf.
The module thermo calculates the energetics from the change in ASA. The total change in ASA is the sum of the ASAp and ASAnp which distinguishes between the contributions of polar and non-polar atoms. These are then used to calculate the change in Cp and Hod for a desired temperature T. From the change in ASA of the different side-chains involved in the dissociation, the conformational entropy gained for the ligand and the enzyme is calculated. Finally, the total entropy change is calculated as the sum of all the entropic contributions.
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