Name
Abstract | ||
|---|---|---|
Protein folding is the physical process by which a sequence of amino acids in a protein folds into its tertiary structure, which determines the functionality of the protein. The knowledge of this structure is crucial for the development of new pharmaceutical therapies. For this reason, many drug industries are interested in applying these kind of algorithms. There are various methods to perform this process, one of the most interesting is Ab Initio modeling. This method creates the 3D-structure from energetic and geometrical features. However, despite its potentiality, companies are slowed down by the high computational needing of the algorithm. A speed-up in the execution time would be crucial to enhance productivity in such industries. In this work we present an accelerated implementation of an Ab Initio Protein Folding Algorithm, based on Monte Carlo simulation. Our implementation is able to reach a speed-up of 1,61x with relation to a pure software implementation, and there is room for more optimization. Furthermore, the algorithm required only 3 weeks to implement, which represents an extremely rapid development time in comparison with typical hardware applications. |
Year | DOI | Venue |
|---|---|---|
2016 | 10.1109/RTSI.2016.7740584 | 2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI) |
Keywords | Field | DocType |
ProFAX,hardware acceleration,amino acid sequence,tertiary structure,pharmaceutical therapies,drug industries,energetic features,geometrical features,ab initio protein folding algorithm,Monte Carlo simulation,software implementation | Monte Carlo method,Protein folding,Algorithm design,Protein tertiary structure,Computer science,Field-programmable gate array,Algorithm,Acceleration,Hardware acceleration,Ab initio | Conference |
ISBN | Citations | PageRank |
978-1-5090-1132-2 | 0 | 0.34 |
References | Authors | |
0 | 3 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Giulia Guidi | 1 | 13 | 1.25 |
| Lorenzo Di Tucci | 2 | 18 | 3.48 |
| Marco D. Santambrogio | 3 | 771 | 91.15 |