Protein Tertiary Structure Prediction

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.

GAc figure 1, useing NetSolve Farming

The above figure illustrates the outline of the system. Each process of Simulated Annealing and energy calculation is performed in each server. The crossover operation is performed at the client. The following picture is an example of protein prediction of C-Peptide.

GAc figure 2, Protein prediction of C-Peptide

Researcher: Tomo Hiroyasu ( )
Institution: Intelligent Systems Design Lab/Doshisha University

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Additional Applications


  Innovative Computing Laboratory
Contact NetSolve: Computer Science Department
  University of Tennessee