Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab
Computer Engineering Department, Iran University of Science and Technology, Tehran, Iran
bioRxiv preprint 2015/07/13/022434, (13 Jul 2015)

   title={Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU},

   author={Khakzad, Hamed and Karami, Yasaman and ARAB, Seyed Shahriar},




   publisher={Cold Spring Harbor Labs Journals}


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Protein tertiary structure prediction (PSP) is one of the most challenging problems in bioinformatics. Different methods have been introduced to solve this problem so far, but PSP is computationally intensive and belongs to the NP-hard class. One of the best solutions to accelerate PSP is the use of a massively parallel processing architecture, such graphical processing unit (GPU), which is used to parallelize computational algorithms. In this paper, we have proposed a parallel architecture to accelerate PSP. A bio-inspired method, particle swarm optimization (PSO) has been used as the optimization method to solve PSP. We have also performed a comprehensive study on implementing different topologies of PSO on GPU to consider the acceleration rate. Our solution belongs to ab-initio category which is based on the dihedral angles and calculates the energy-levels to predict the tertiary structure. Indeed, we have studied the search space of a protein to find the best pair of angles that gives the minimum free energy. A profile-level knowledge-based force field based on PSI-BLAST multiple sequence alignment has been applied as a fitness function to calculate the energy values. Different topologies and variations of PSO are considered here and the experimental results show that the speedup gain using GPU is about 34 times faster than CPU implementation of the algorithm with an acceptable precision. The energy values of predicted structures confirm the robustness of the algorithm.
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