Title :
Preliminary Steps Towards Protein Folding Prediction Using Reconfigurable Computing
Author :
Armstrong, Nilton B., Jr. ; Lopes, Heitor S. ; Lima, Carlos R Erig
Author_Institution :
Bioinformatics Lab. & Electron. Dept., Fed. Univ. of Technol. - Parana, Curitiba
Abstract :
This paper presents methodologies for the design of a system based on reconfigurable hardware applied to a complex problem in molecular biology: the protein folding problem. Different approaches are explored and advantages and drawbacks are analyzed. Efficient strategies are devised to achieve a significant reduction of the search space of possible foldings. Several simulations are done to evaluate the performance of the system as well as the demand for FPGA´s resources. This work is the base for future hardware implementations aiming at finding the optimal solution for protein folding problems using the 2D-HP model
Keywords :
biology computing; field programmable gate arrays; molecular biophysics; proteins; reconfigurable architectures; 2D-HP model; FPGA; molecular biology; optimal solution; protein folding prediction; reconfigurable computing; Amino acids; Bioinformatics; Biological system modeling; Biology computing; Field programmable gate arrays; Hardware; Lattices; Predictive models; Proteins; Sequences;
Conference_Titel :
Reconfigurable Computing and FPGA's, 2006. ReConFig 2006. IEEE International Conference on
Conference_Location :
San Luis Potosi
Print_ISBN :
1-4244-0690-0
Electronic_ISBN :
1-4244-0690-0
DOI :
10.1109/RECONF.2006.307758
