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Volumn , Issue , 2006, Pages

A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID FIBRIL; COULOMB FORCE; NUCLEUS; PRION; TFLOPS;

EID: 34548274117     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1188455.1188506     Document Type: Conference Paper
Times cited : (57)

References (39)
  • 1
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • M. Karplus and J. A. McCammon, "Molecular dynamics simulations of biomolecules," Nat Struct Biol, vol. 9, pp. 646-52, 2002.
    • (2002) Nat Struct Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 2
    • 33749169503 scopus 로고    scopus 로고
    • A highly parallelized special-purpose computer for many-body simulations with an arbitrary central force: MD-GRAPE
    • T. Fukushige, M. Taiji, J. Makino, T. Ebisuzaki, and D. Sugimoto, "A highly parallelized special-purpose computer for many-body simulations with an arbitrary central force: MD-GRAPE," Astrophys J, vol. 468, pp. 51-61, 1996.
    • (1996) Astrophys J , vol.468 , pp. 51-61
    • Fukushige, T.1    Taiji, M.2    Makino, J.3    Ebisuzaki, T.4    Sugimoto, D.5
  • 4
    • 84877051133 scopus 로고    scopus 로고
    • Protein Explorer: A PetaFLOPS Special-Purpose Computer System for Molecular Dynamics Simulations
    • Phoenix, AZ, USA, on CD-ROM
    • M. Taiji, T. Narumi, Y. Ohno, N. Futatsugi, A. Suenaga, N. Takada, and A. Konagaya, "Protein Explorer: A PetaFLOPS Special-Purpose Computer System for Molecular Dynamics Simulations," in Supercomputing 2003, Phoenix, AZ, USA, 2003, on CD-ROM, http://www.sc-conference.org/sc2003/paperpdfs/pap168.pdf.
    • (2003) Supercomputing 2003
    • Taiji, M.1    Narumi, T.2    Ohno, Y.3    Futatsugi, N.4    Suenaga, A.5    Takada, N.6    Konagaya, A.7
  • 5
    • 0035961329 scopus 로고    scopus 로고
    • The structural basis of protein folding and its links with human disease
    • C. M. Dobson, "The structural basis of protein folding and its links with human disease," Philos Trans R Soc Land B Biol Sci, vol. 356, pp. 133-45, 2001.
    • (2001) Philos Trans R Soc Land B Biol Sci , vol.356 , pp. 133-145
    • Dobson, C.M.1
  • 6
    • 0036238472 scopus 로고    scopus 로고
    • Towards an understanding of amyloidogenesis
    • J. W. Kelly, "Towards an understanding of amyloidogenesis," Nat Struct Biol, vol. 9, pp. 323-5, 2002.
    • (2002) Nat Struct Biol , vol.9 , pp. 323-325
    • Kelly, J.W.1
  • 7
    • 0036377156 scopus 로고    scopus 로고
    • Amyloid-fibril formation. Proposed mechanisms and relevance to conformational disease
    • E. Zerovnik, "Amyloid-fibril formation. Proposed mechanisms and relevance to conformational disease," Eur J Biochem, vol. 269, pp. 3362-71, 2002.
    • (2002) Eur J Biochem , vol.269 , pp. 3362-3371
    • Zerovnik, E.1
  • 8
    • 0030586945 scopus 로고    scopus 로고
    • Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous beta-sheet helix
    • C. Blake and L. Serpell, "Synchrotron X-ray studies suggest that the core of the transthyretin amyloid fibril is a continuous beta-sheet helix," Structure, vol. 4, pp. 989-98, 1996.
    • (1996) Structure , vol.4 , pp. 989-998
    • Blake, C.1    Serpell, L.2
  • 9
    • 0031962158 scopus 로고    scopus 로고
    • Structural analysis of Alzheimer's beta(1-40) amyloid: Protofilament assembly of tubular fibrils
    • S. B. Malinchik, H. Inouye, K. E. Szumowski, and D. A. Kirschner, "Structural analysis of Alzheimer's beta(1-40) amyloid: protofilament assembly of tubular fibrils," Biophys J, vol. 74, pp. 537-45, 1998.
    • (1998) Biophys J , vol.74 , pp. 537-545
    • Malinchik, S.B.1    Inouye, H.2    Szumowski, K.E.3    Kirschner, D.A.4
  • 10
    • 0035956924 scopus 로고    scopus 로고
    • An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid
    • M. Balbirnie, R. Grothe, and D. S. Eisenberg, "An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated beta-sheet structure for amyloid," Proc Natl Acad Sci U S A, vol. 98, pp. 2375-80, 2001.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 2375-2380
    • Balbirnie, M.1    Grothe, R.2    Eisenberg, D.S.3
  • 12
    • 0029780647 scopus 로고    scopus 로고
    • Support for the prion hypothesis for inheritance of a phenotypic trait in yeast
    • M. M. Patino, J. J. Liu, J. R. Glover, and S. Lindquist, "Support for the prion hypothesis for inheritance of a phenotypic trait in yeast," Science, vol. 273, pp. 622-6, 1996.
    • (1996) Science , vol.273 , pp. 622-626
    • Patino, M.M.1    Liu, J.J.2    Glover, J.R.3    Lindquist, S.4
  • 13
    • 0028308104 scopus 로고
    • URE3] as an altered URE2 protein: Evidence for a prion analog in Saccharomyces cerevisiae
    • R. B. Wickner, "[URE3] as an altered URE2 protein: evidence for a prion analog in Saccharomyces cerevisiae," Science, vol. 264, pp. 566-9, 1994.
    • (1994) Science , vol.264 , pp. 566-569
    • Wickner, R.B.1
  • 14
    • 0028351003 scopus 로고
    • Polypeptide chain termination in Saccharomyces cerevisiae
    • I. Stansfield and M. F. Tuite, "Polypeptide chain termination in Saccharomyces cerevisiae," Curr Genet, vol. 25, pp. 385-95, 1994.
    • (1994) Curr Genet , vol.25 , pp. 385-395
    • Stansfield, I.1    Tuite, M.F.2
  • 16
    • 1642617641 scopus 로고    scopus 로고
    • Protein-only transmission of three yeast prion strains
    • C. Y. King and R. Diaz-Avalos, "Protein-only transmission of three yeast prion strains," Nature, vol. 428, pp. 319-23, 2004.
    • (2004) Nature , vol.428 , pp. 319-323
    • King, C.Y.1    Diaz-Avalos, R.2
  • 17
  • 18
    • 1642633056 scopus 로고    scopus 로고
    • Conformational variations in an infectious protein determine prion strain differences
    • M. Tanaka, P. Chien, N. Naber, R. Cooke, and J. S. Weissman, "Conformational variations in an infectious protein determine prion strain differences," Nature, vol. 428, pp. 323-8, 2004.
    • (2004) Nature , vol.428 , pp. 323-328
    • Tanaka, M.1    Chien, P.2    Naber, N.3    Cooke, R.4    Weissman, J.S.5
  • 19
    • 0033582587 scopus 로고    scopus 로고
    • Thermodynamics of model prions and its implications for the problem of prion protein folding
    • P. M. Harrison, H. S. Chan, S. B. Prusiner, and F. E. Cohen, "Thermodynamics of model prions and its implications for the problem of prion protein folding," J Mol Biol, vol. 286, pp. 593-606, 1999.
    • (1999) J Mol Biol , vol.286 , pp. 593-606
    • Harrison, P.M.1    Chan, H.S.2    Prusiner, S.B.3    Cohen, F.E.4
  • 20
    • 10844230140 scopus 로고    scopus 로고
    • Replica exchange molecular dynamics simulations of amyloid peptide aggregation
    • M. Cecchini, F. Rao, M. Seeber, and A. Caflisch, "Replica exchange molecular dynamics simulations of amyloid peptide aggregation," J Chem Phys, vol. 121, pp. 10748-56, 2004.
    • (2004) J Chem Phys , vol.121 , pp. 10748-10756
    • Cecchini, M.1    Rao, F.2    Seeber, M.3    Caflisch, A.4
  • 21
    • 0037048673 scopus 로고    scopus 로고
    • Solvent environment conducive to protein aggregation
    • A. Fernandez and M. De Las Mercedes Boland, "Solvent environment conducive to protein aggregation," FEBS Lett, vol. 529, pp. 298-301, 2002.
    • (2002) FEBS Lett , vol.529 , pp. 298-301
    • Fernandez, A.1    De Las Mercedes Boland, M.2
  • 22
    • 19444380574 scopus 로고    scopus 로고
    • Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: Simulation by reaction path annealing
    • J. Lipfert, J. Franklin, F. Wu, and S. Doniach, "Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing," J Mol Biol, vol. 349, pp. 648-58, 2005.
    • (2005) J Mol Biol , vol.349 , pp. 648-658
    • Lipfert, J.1    Franklin, J.2    Wu, F.3    Doniach, S.4
  • 23
    • 0036784617 scopus 로고    scopus 로고
    • Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation
    • B. Ma and R. Nussinov, "Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation," Protein Sci, vol. 11, pp. 2335-50, 2002.
    • (2002) Protein Sci , vol.11 , pp. 2335-2350
    • Ma, B.1    Nussinov, R.2
  • 24
    • 0037195098 scopus 로고    scopus 로고
    • Stabilities and conformations of Alzheimer's beta-amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects
    • B. Ma and R. Nussinov, "Stabilities and conformations of Alzheimer's beta-amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects," Proc Natl Acad Sci USA, vol. 99, pp. 14126-31, 2002.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14126-14131
    • Ma, B.1    Nussinov, R.2
  • 26
    • 65649129896 scopus 로고    scopus 로고
    • MDGRAPE-3 chip: A 165 GFLOPS Application Specific LSI for Molecular Dynamics Simulations
    • Stanford University, CA, USA
    • M. Taiji, "MDGRAPE-3 chip: a 165 GFLOPS Application Specific LSI for Molecular Dynamics Simulations," in Hot Chips 16, Stanford University, CA, USA, 2004.
    • (2004) Hot Chips , vol.16
    • Taiji, M.1
  • 30
    • 1242346370 scopus 로고
    • The missing term in effective pair potentials
    • J. C. H. Berendsen, R. J. Grigera, and P. T. Straatsma, "The missing term in effective pair potentials," J Phys Chem, vol. 91, pp. 6269-71, 1987.
    • (1987) J Phys Chem , vol.91 , pp. 6269-6271
    • Berendsen, J.C.H.1    Grigera, R.J.2    Straatsma, P.T.3
  • 31
    • 34548204018 scopus 로고    scopus 로고
    • http://atlas.riken.jp/~susukita/
  • 32
    • 33751242883 scopus 로고
    • Speeding up N-body calculations on machines lacking a hardware square root
    • A. H. Karp, "Speeding up N-body calculations on machines lacking a hardware square root," Scientific Programming, vol. 1, pp. 133-41, 1992.
    • (1992) Scientific Programming , vol.1 , pp. 133-141
    • Karp, A.H.1
  • 33
    • 0003714666 scopus 로고    scopus 로고
    • Pentium Pro Inside: I. A Treecode at 430 GigaFLOPS on ASCI Red II. Price/Performance of $50/Mflop on Loki and Hyglac
    • 97, San Jose, on CD-ROM
    • M. S. Warren, J. K. Salmon, D. J. Becker, M. P. Goda, T. Sterling, and G. S. Winckelmans, "Pentium Pro Inside: I. A Treecode at 430 GigaFLOPS on ASCI Red II. Price/Performance of $50/Mflop on Loki and Hyglac," in Proc. Supercomputing '97, San Jose, 1997, on CD-ROM.
    • (1997) Proc. Supercomputing
    • Warren, M.S.1    Salmon, J.K.2    Becker, D.J.3    Goda, M.P.4    Sterling, T.5    Winckelmans, G.S.6
  • 34
    • 69549103939 scopus 로고    scopus 로고
    • Avalon: An Alpha/Linux Cluster Achieves 10 Gflops for $150k
    • 98, Orlando, on CD-ROM
    • M. S. Warren, T. C. Germann, P. S. Lomdahl, and D. M. Beazley, "Avalon: An Alpha/Linux Cluster Achieves 10 Gflops for $150k," in Proc. Supercomputing '98, Orlando, 1998, on CD-ROM.
    • (1998) Proc. Supercomputing
    • Warren, M.S.1    Germann, T.C.2    Lomdahl, P.S.3    Beazley, D.M.4
  • 35
    • 33646398648 scopus 로고    scopus 로고
    • $7.0/Mflops Astrophysical N-Body Simulation with Treecode on GRAPE-5
    • 99, Portland, on CD-ROM
    • A. Kawai, T. Fukushige, and J. Makino, "$7.0/Mflops Astrophysical N-Body Simulation with Treecode on GRAPE-5," in Proc. Supercomputing '99, Portland, 1999, on CD-ROM.
    • (1999) Proc. Supercomputing
    • Kawai, A.1    Fukushige, T.2    Makino, J.3
  • 37
    • 38849187462 scopus 로고    scopus 로고
    • 25 Tflop/s Multibillion-Atom Molecular Dynamics Simulations and Visualization/Analysis on BlueGene/L
    • Seattle, on CD-ROM
    • T. C. Germann, K. Kadau, and P. S. Lomdahl, "25 Tflop/s Multibillion-Atom Molecular Dynamics Simulations and Visualization/Analysis on BlueGene/L," in Proc. Supercomputing 2005, Seattle, 2005, on CD-ROM, http://sc05.supercomputing.org/schedule/pdf/pap122.pdf.
    • (2005) Proc. Supercomputing
    • Germann, T.C.1    Kadau, K.2    Lomdahl, P.S.3


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