Bernard Brocka
ABSTRACT
Structural motifs refer to patterns in 3D space that bear biological significance as they can indicate regions in the protein that have important roles in biochemical functions. Finding structural motifs given a set of peptides are NP-hard. Thus, there is no known polynomial-time algorithm that solves the problem optimally except when the quality of the solution is compromised. Although computationally hard, the problem is approximable and has a known polynomial-time approximation scheme (PTAS). With an existing PTAS, the problem can have a guaranteed quality that is inversely proportional to the running time. For a small error bound, the running time of the algorithm can become impractical. In this study, we design and implement a parallel version of the PTAS for the (R-C)-compact structural motif problem. Based on the empirical results, we obtained a speedup between 4x - 5x from the sequential version of the algorithm using three different protein data sets.
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Index Terms
- Parallel Polynomial-Time Approximation Scheme (PTAS) for Finding Compact Structural Motifs
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