论文信息 - Preliminary Steps Towards Protein Folding Prediction Using Reconfigurable Computing

Preliminary Steps Towards Protein Folding Prediction Using Reconfigurable Computing

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

Heitor Silvério Lopes | Carlos R. Erig Lima | Nilton B. Armstrong

[1] Heitor Silvério Lopes,et al. An Enhanced Genetic Algorithm for Protein Structure Prediction Using the 2D Hydrophobic-Polar Model , 2005, Artificial Evolution.

[2] Mihalis Yannakakis,et al. On the Complexity of Protein Folding , 1998, J. Comput. Biol..

[3] Bertil Schmidt,et al. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW , 2005, Bioinform..

[4] Vittorio Rosato,et al. Designing hardware for protein sequence analysis , 2003, Bioinform..

[5] D. A. Harris,et al. Principles of Biochemistry (2nd edn) , 1993 .

[6] Eduardo Sanchez,et al. Performing DNA comparison on a bio-inspired tissue of FPGAs , 2003, Proceedings International Parallel and Distributed Processing Symposium.

[7] A. Lehninger. Principles of Biochemistry , 1984 .

[8] Frank Thomson Leighton,et al. Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.

[9] Akihiko Konagaya,et al. High Speed Homology Search with FPGAs , 2001, Pacific Symposium on Biocomputing.

[10] K. Dill. Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[11] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.