-
1
-
-
0036725277
-
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
-
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
-
3
-
-
85105740186
-
1.34 TFLOPS Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM
-
on CD-ROM
-
T. Narumi, R. Susukita, T. Koishi, K. Yasuoka, H. Furusawa, A. Kawai, and T. Ebisuzaki, "1.34 TFLOPS Molecular Dynamics Simulation for NaCl with a Special-Purpose Computer: MDM," in Proc. Supercomputing 2000, 2000, on CD-ROM.
-
(2000)
Proc. Supercomputing
-
-
Narumi, T.1
Susukita, R.2
Koishi, T.3
Yasuoka, K.4
Furusawa, H.5
Kawai, A.6
Ebisuzaki, T.7
-
4
-
-
84877051133
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
11
-
-
0038690113
-
Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide
-
R. Diaz-Avalos, C. Long, E. Fontano, M. Balbirnie, R. Grothe, D. Eisenberg, and D. L. Caspar, "Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide," J Mol Biol, vol. 330, pp. 1165-75, 2003.
-
(2003)
J Mol Biol
, vol.330
, pp. 1165-1175
-
-
Diaz-Avalos, R.1
Long, C.2
Fontano, E.3
Balbirnie, M.4
Grothe, R.5
Eisenberg, D.6
Caspar, D.L.7
-
12
-
-
0029780647
-
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
-
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
-
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
-
15
-
-
20444440728
-
Structure of the cross-beta spine of amyloid-like fibrils
-
R. Nelson, M. R. Sawaya, M. Balbirnie, A. O. Madsen, C. Riekel, R. Grothe, and D. Eisenberg, "Structure of the cross-beta spine of amyloid-like fibrils," Nature, vol. 435, pp. 773-8, 2005.
-
(2005)
Nature
, vol.435
, pp. 773-778
-
-
Nelson, R.1
Sawaya, M.R.2
Balbirnie, M.3
Madsen, A.O.4
Riekel, C.5
Grothe, R.6
Eisenberg, D.7
-
16
-
-
1642617641
-
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
-
-
0034714351
-
Nucleated conformational conversion and the replication of conformational information by a prion determinant
-
T. R. Serio, A. G. Cashikar, A. S. Kowal, G. J. Sawicki, J. J. Moslehi, L. Serpell, M. F. Arnsdorf, and S. L. Lindquist, "Nucleated conformational conversion and the replication of conformational information by a prion determinant," Science, vol. 289, pp. 1317-21, 2000.
-
(2000)
Science
, vol.289
, pp. 1317-1321
-
-
Serio, T.R.1
Cashikar, A.G.2
Kowal, A.S.3
Sawicki, G.J.4
Moslehi, J.J.5
Serpell, L.6
Arnsdorf, M.F.7
Lindquist, S.L.8
-
18
-
-
1642633056
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
27
-
-
30344440627
-
-
San Francisco: University of California
-
D. A. Case, T. A. Danden, I. T. E. Cheatham, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, B. Wang, D. A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Veroza, C. Schafmeister, J. W. Caldwell, W. S. Ross, and P. A. Kollman, "AMBER 8." San Francisco: University of California, 2004.
-
(2004)
AMBER
, vol.8
-
-
Case, D.A.1
Danden, T.A.2
Cheatham, I.T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Wang, B.9
Pearlman, D.A.10
Crowley, M.11
Brozell, S.12
Tsui, V.13
Gohlke, H.14
Mongan, J.15
Hornak, V.16
Cui, G.17
Veroza, P.18
Schafmeister, C.19
Caldwell, J.W.20
Ross, W.S.21
Kollman, P.A.22
more..
-
28
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules
-
W. D. Cornel, P. Cieplak, C. I. Bayly, I. R. Gould, J. K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules," J Am Chem Soc, vol. 117, pp. 5179-97, 1995.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornel, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, J.K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
29
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, "Comparison of simple potential functions for simulating liquid water," J Chem Phys, vol. 79, pp. 926-35, 1983.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
30
-
-
1242346370
-
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
-
-
http://atlas.riken.jp/~susukita/
-
-
-
-
32
-
-
33751242883
-
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
-
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
-
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
-
$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
-
36
-
-
38849108992
-
100+ TFlop Solidification Simulations on BlueGene/L
-
Seattle, on CD-ROM
-
F. H. Streitz, J. N. Glosli, M. V. Patel, B. Chan, R. K. Yates, B. R. D. Supinski, J. Sexton, and J. A. Gunnels, "100+ TFlop Solidification Simulations on BlueGene/L," in Proc. Supercomputing 2005, Seattle, 2005, on CD-ROM, http://sc05.supercomputing.org/schedule/pdf/pap307.pdf.
-
(2005)
Proc. Supercomputing
-
-
Streitz, F.H.1
Glosli, J.N.2
Patel, M.V.3
Chan, B.4
Yates, R.K.5
Supinski, B.R.D.6
Sexton, J.7
Gunnels, J.A.8
-
37
-
-
38849187462
-
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
-
38
-
-
34548234438
-
Folding dynamics of 10-residue mini-protein
-
submitted
-
A. Suenaga, T. Narumi, N. Futatsugi, R. Yanai, Y. Ohno, N. Okimoto, and M. Taiji, "Folding dynamics of 10-residue mini-protein," submitted, 2006.
-
(2006)
-
-
Suenaga, A.1
Narumi, T.2
Futatsugi, N.3
Yanai, R.4
Ohno, Y.5
Okimoto, N.6
Taiji, M.7
-
39
-
-
33645109502
-
Structure and dynamics of RNA polymerase II elongation complex
-
A. Suenaga, N. Okimoto, N. Futatsugi, Y. Hirano, T. Narumi, Y. Ohno, R. Yanai, T. Hirokawa, T. Ebisuzaki, A. Konagaya, and M. Taiji, "Structure and dynamics of RNA polymerase II elongation complex," Biochem Biophys Res Commun, vol. 343, pp. 90-8, 2006.
-
(2006)
Biochem Biophys Res Commun
, vol.343
, pp. 90-98
-
-
Suenaga, A.1
Okimoto, N.2
Futatsugi, N.3
Hirano, Y.4
Narumi, T.5
Ohno, Y.6
Yanai, R.7
Hirokawa, T.8
Ebisuzaki, T.9
Konagaya, A.10
Taiji, M.11
|