High Performance Research Projects on the Helix Systems

High Performance Computing
Research Projects on the Helix Systems

The high performance computing capabilities of the Helix Systems
are being utilized by the NIH scientific community for research projects
in diverse areas.

Publications from 2004 to current

2003

Hydrogen bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay. Lee YS, Hodoscek M, Kador PF, Sugiyama K. Chem. Biol. Interact, 143-144:307-16. (2003).
A Random Effects Transition Model For Longitudinal Binary Data With Informative Missingness. Paul S Albert & Dean Follmann. Statistica Neerlandica, 57 Issue 1 Page 100-111, (2003).
On the kinematics of protein folding. Sean Cahill, Michael Cahill, Kevin Cahill. J. Comp. Chem, Volume 24, Issue 11, Pages 1364-1370 (2003).
Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides. Dixon AM, Venable R, Widmalm G, Bull TE, Pastor RW. Biopolymers, 69(4):448-60. (2003).
Modeling tumor growth with random onset. Albert PS, Shih JH. Biometrics. 2003 Dec 59(4):897-906.
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Zanuy D, Ma B, Nussinov R. Biophys J. 2003 Mar;84(3):1884-94.
The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. Zanuy D, Nussinov R. J Mol Biol. 2003 Jun 6;329(3):565-84.
Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants. Ma B, Nussinov R. Protein Eng. 2003 Aug;16(8):561-75.
A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR. J Struct Biol. 2003 Jan;141(1):63-76.
Interdepend ence of backbone flexibility, residue conservation, and enzyme function: a case study on beta1,4-galactosyltransferase-I. Gunasekaran K, Ma B, Ramakrishnan B, Qasba PK, Nussinov R.Biochemistry. 2003 Apr 8;42(13):3674-87.
Triggering loops and enzyme function: identification of loops that trigger and modulate movements. Gunasekaran K, Ma B, Nussinov R. J Mol Biol. 2003 Sep 5;332(1):143-59.
Synthesis and conformational analysis of a locked analogue of carbovir built on a bicyclo[3.1.0]hex-2-enyl template. Choi Y, Sun G, George C, Nicklaus MC, Kelley JA, Marquez VE. Nucleotides Nucleic Acids. 2003 Dec;22(12):2077-91.
Direct Observation of the Folding and Unfolding of a Hairpin in Explicit Water through Computer Simulation. Xiongwu Wu, Shaomeng Wang, and Bernard R. Brooks. J. Am. Chem. Soc. May 15;124(19):5282-3.
Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS. PLoS Biol. 2003 Dec;1(3):E74.

2002

Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study. Dixon AM, Venable RM, Pastor RW, Bull TE. Biopolymers, 65(4):284-98. (2002).
Parametric and semiparametric approaches to testing for seasonal trend in serial count data. Hunsberger S, Albert PS, Follmann DA, Suh E. Biostatistics. 2002 Jun;3(2):289-98.
Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. VanBuren V, Piao Y, Dudekula DB, Qian Y, Carter MG, Martin PR, Stagg CA, Bassey UC, Aiba K, Hamatani T, Kargul GJ, Luo AG, Kelso J, Hide W, Ko MS.Genome Res. 2002 Dec;12(12):1999-2003.
A Latent Autoregressive Model for Longitudinal Binary Data Subject to Informative Missingness. Albert, PS, Follmann, DA, Wang, SA, Suh, EB. Biometrics, 58 Issue 3 Page 631-642 (2002).
A preliminary transcriptome map of non-small cell lung cancer. Fujii T, Dracheva T, Player A, Chacko S, Clifford R, Strausberg RL, Buetow K, Azumi N, Travis WD, Jen J. Cancer Res. 2002 Jun 15;62(12):3340-6.
Mutant deoxynucleotide carrier is associated with congenital microcephaly. Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schaffer AA, Biesecker LG. Nat Genet. 2002 Sep;32(1):175-9.
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. Yeh IC, Hummer G. J Am Chem Soc. 2002 Jun 12;124(23):6563-8.

2001

Simultaneous Determination of Orientational and Order Parameter Distributions from NMR Spectra of Partially Oriented Model Membranes. Edward Sternin, Hartmut Schafer, Ivan V. Polozov and Klaus Gawrisch. J. Mag. Res, 149(1), 110-113 (2001).
Circularly permuted proteins in the protein structure database. Jongsun Jung and Byungkook Lee. Protein Science, 10:1881-1886. (2001).
PET, CT, and MR image registration of the rat brain and skull. Vaquero, J.J. Desco, M. Pascau, J. Santos, A. Injae Lee Seidel, J. Green, M.V. Nuclear Science, IEEE Transactions, 48, 1440-1445. (2001).
Crystal structure of the 14-3-3zeta:serotonin N-acetyltransferase complex. a role for scaffolding in enzyme regulation. Obsil T, Ghirlando R, Klein DC, Ganguly S, Dyda F. Cell. 2001 Apr 20;105(2):257-67.

2000

Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils. Antzutkin ON, Balbach JJ, Leapman RD, Rizzo NW, Reed J, Tycko R. Proc Natl Acad Sci U S A. 2000 Nov 21;97(24):13045-50.
Amyloid fibril formation by A beta 16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R. Biochemistry 2000 Nov 14;39(45):13748-59.
Multivariate measurement of gene expression relationships. Kim S, Dougherty ER, Chen Y, Sivakumar K, Meltzer P, Trent JM, Bittner M. Genomics. 2000 Jul 15;67(2):201-9.
Theoretical formalism for kinesin motility I. Bead movement powered by single one-headed kinesins. Chen Y. Biophys J. 2000 Jan;78(1):313-21.

1999

Asymmetry and direction reversal in fluctuation-induced biased Brownian motion.Chen YD, Yan B, Miura R. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Oct;60(4 Pt A):3771-5.
Expression profiling using cDNA microarrays. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Nat Genet. 1999 Jan;21(1 Suppl):10-4. Review.

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High Performance Computing Research Projects on the Helix Systems

2003

2002

2001

2000

1999

High Performance Computing
Research Projects on the Helix Systems