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Conclusions:
- Analytical calculation of the solvent accessible surface areas and
their derivatives (ASAD) has been simplified due to the new vector
parametrization.
- CPU time spent on ASAD calculations can be greatly reduced by
employing new algorithm of finding the vertices of Gauss-Bonnet path
by calculating the intersection of half-spaces.
- Protein-solvent interaction is an extraordinarily important factor
in computational studies of protein folding. Energy minimization without
solvent is successful in mathematical sense, but it does not allow one to
find the native structure. On the other hand, inclusion of solvent smoothes
low energy local minima for unfolded structures and therefore drives
structure minimization towards a folded state.
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