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Protein is a substance directly connected to the biological phenomena and its biological functions are said
to be derived from its tertiary structure. Thus, clarification of its tertiary structure leads to an
explanation of the biological phenomena process. It is rather easy to determine the sequences of the
amino acids that the protein consists of. On the other hand, it is very difficult to determine the
tertiary structure. The tertiary structure of the protein is believed to correspond to the conformation
with the lowest residual potential energy. Therefore, in this system, the protein tertiary structure is
determined by minimizing the total energy of the protein. KONF90 is used for deriving the energy of
a protein. PSA/GAc is used as the optimization tool. PSA/GAc is a hybrid method of Parallel Simulated
annealing and Genetic Algorithm.
Since PSA/GAc needs a lot of iterations, it takes a long time to derive the optimum solution.
To solve this problem, NetSolve is used. NetSolve is Grid RPC middleware. NetSolve has a
function called Farming which is very suitable for this system and calculations to be performed
very efficiently.
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