Drug design issues on the Cell BE

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4917 LNCS, Issue , 2008, Pages 176-190

  Servat, Harald ^a   González Alvarez, Cecilia ^b   Aguilar, Xavier ^a   Cabrera Benitez, Daniel ^b   Jiménez González, Daniel ^b  

^a BARCELONA SUPERCOMPUTING CENTER   (Spain)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-MEDICAL APPLICATIONS; CHALLENGING PROBLEM; DRUG DESIGNS; EMBEDDED ARCHITECTURES; FOURIER; INTERNATIONAL CONFERENCES; MEMORY ACCESSES; PARALLELIZATION; PERFORMANCE IMPACTS; PROTEIN DOCKING; TIME-CONSUMING PROCESSES;

APPROXIMATION ALGORITHMS; BIOINFORMATICS; CELLS; CHEMOTHERAPY; COMPUTER ARCHITECTURE; COMPUTER SCIENCE; COMPUTER SYSTEMS; CYTOLOGY; DOCKING; DRUG DELIVERY; DRUG DOSAGE; FOURIER TRANSFORMS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INFORMATION SCIENCE; PROCESS ENGINEERING;

PROGRAM COMPILERS;

EID: 49949114758     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-77560-7_13     Document Type: Conference Paper

References (24)

1. http://CellPerformance.com
2. Cell broadband engine programming handbook vl.0
3. Bellens, P., Perez, J.M., Badia, R.M., Labarta, J.: CellSs: A programming model for the cell be architecture. In: Conference on Supercomputing (2006)
4. Blagojevic, F., et al.: Dynamic multigrain parallelization on the cell broadband engine. In: PPoPP (2007)
5. Blagojevic, F., et al.: RAxML-Cell: Parallel phylogenetic tree inference on the cell broadband engine. In: Proceedings of the 21st IEEE/ACM International Parallel and Distributed Processing Symposium (2007)
6. Chelliah, V., et al.: Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. In: JMB 357 (2006)
7. Chen, T., et al.: Cell broadband engine architecture and its first implementation
8. Choi, J., et al.: Parallel matrix transpose algorithms on distributed memory concurrent computers. Parallel Computing 21(9), 1387-1405 (1995)
9. Chow, A.C., et al.: A programming example: Large FFT on the cell broadband engine. White Paper IBM (2005)
10. Eklundh, J.: A fast computer method for matrix transposing. IEEE transactions on computers 21, 801-803 (1972)
11. Eleftheriou, M., et al.: Scalable framework for 3D FFTs on the blue gene/1 supercomputer: Implementation and early performance measurements. IBM J. RES. & DEV 49(2/3) (2005)
12. Fernández-Recio, J., Totrov, M., Abagyan, R.: Soft protein-protein docking in internal coordinates. Protein Science 11V, 280-291 (2002)
13. Flachs, B., et al.: The Microarchitecture of the Synergistic Processor for a Cell Processor. IEEE Journal of Solid-State Circuits 41(1)V (2006)
14. Gabb, H.A., et al.: Modelling protein docking usign shape complementary, electrostatics and biochemical information. J. Mol. Biol. 272 (1997)
15. Govindaraju, N.K., et al.: A memory model for scientific algorithms on graphics processors. In: Proceedings of the 2006 ACM/IEEE conference on Supercomputing, p. 89. ACM Press, New York (2006)
16. Greene, J., Cooper, R.: A parallel 64k complex FFT algorithm for the ibm/sony/toshiba cell broadband engine processor. In: Tech. Conf. Proc. of the Global Signal Processing Expo (GSPx) (2005)
17. Gschwind, M., et al: Synergistic Processing in Cell's Multicore Architecture. IEEE Micro 26(2) (March 2006)
18. Jimenez-Gonzalez, D., et al.: Performance analysis of cell broadband engine for high memory bandwidth applications. In: ISPASS (2007)
19. Kahle, J.A., et al: Introduction to the Cell multiprocessor. IBM Journal of Research and Development 49(4/5) (2005)
20. Katchalski-Katzir, E., et al.: Molecular sufrace recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. USA, Biohphysics 89, 2195-2199 (1992)
21. Knuth, D.: The art of computer programming: Sorting and searching. Addison-Wesley Publishing Company 3 (1973)
22. Krolak, D.: Unleashing the cell broadband engine processor. MPR Fall Processor Forum (November 2005)
23. Naga, K., Govindaraju, D.M.: Cache-Efficient Numerical Algorithms using Graphics Hardware. Tech. rep., UNC (2007)
24. Wang, D.: Cell mircroprocessor iii. Real World Technologies (2005)