Abstract
In attempts to predict the tertiary structure of proteins we use almost exclusively metaheuristics. However, despite known differences in performance of metaheuristics for different problems, the effect of the choice of metaheuristic has received precious little attention in this field. Particularly parallel implementations have been demonstrated to generally outperform their sequential counterparts, but they are nevertheless used to a much lesser extent for protein structure prediction. In this work we focus strictly on parallel algorithms for protein structure prediction and propose a parallel algorithm, which adds an iterative layer to the traditional niche genetic algorithm. We implement both the traditional niche genetic algorithm and the parallel tempering algorithm in a fashion that allows us to compare the algorithms and look at how they differ in performance. The results show that the iterative niche algorithm converges much faster at lower energy structures than both the traditional niche genetic algorithm and the parallel tempering algorithm.
| Original language | English |
|---|---|
| Title of host publication | Proceedings of the First International Conference on Bioinformatics |
| Number of pages | 7 |
| Volume | 1 |
| Publisher | SCITEPRESS Digital Library |
| Publication date | 2010 |
| Pages | 226-232 |
| ISBN (Print) | 978-989-674-019-1 |
| DOIs | |
| Publication status | Published - 2010 |
| Event | 1st International Conference on Bioinformatics - Valencia, Spain Duration: 20 Jan 2010 → 23 Jan 2010 Conference number: 1 |
Conference
| Conference | 1st International Conference on Bioinformatics |
|---|---|
| Number | 1 |
| Country/Territory | Spain |
| City | Valencia |
| Period | 20/01/2010 → 23/01/2010 |
Keywords
- Genetic algorithm
- Parallel tempering
- Parallelism
- Protein structure prediction