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51

Coarse-Grained Simulations of Nucleoid Structure

Earnest, Tyler M., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 84 KB

english, 2014

52

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

Hallock, Michael J., Stone, John E., Roberts, Elijah, Fry, Corey, Luthey-Schulten, Zaida

Journal:

Parallel Computing

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

53

Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene

Assaf, Michael, Roberts, Elijah, Luthey-Schulten, Zaida, Goldenfeld, Nigel

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 58 KB

english, 2014

54

Translation in the RNA World: Insight from the Proto-Ribosome Model

Chen, Ke, Wang, Bo, Fei, Jingyi, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 43 KB

english, 2014

55

Hierarchical Folding of the rRNA in the Early Assembly of the E. Coli Ribosomal Small Subunit

Lai, Jonathan, Chen, Ke, Kim, Hajin, Ha, Taejkip, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 39 KB

english, 2014

56

Toward a Spatially-Resolved Model of Metabolism in Dense Bacterial Colonies

Cole, John A., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 60 KB

english, 2014

57

Foldons, Protein Structural Modules, and Exons

Anna R. Panchenko, Zaida Luthey-Schulten and Peter G. Wolynes

Journal:

Proceedings of the National Academy of Sciences

Year:

1996

Language:

english

File:

PDF, 1.17 MB

english, 1996

58

Self-Consistently Optimized Energy Functions for Protein Structure Prediction by Molecular Dynamics

Kristin K. Koretke, Zaida Luthey-Schulten and Peter G. Wolynes

Journal:

Proceedings of the National Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 1.78 MB

english, 1998

59

Evaluating protein structure-prediction schemes using energy landscape theory

Eastwood, M. P., Hardin, C., Luthey-Schulten, Z., Wolynes, P. G.

Journal:

IBM Journal of Research and Development

Year:

2001

Language:

english

File:

PDF, 1.33 MB

english, 2001

60

A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase †

Amaro, Rommie E., Sethi, Anurag, Myers, Rebecca S., Davisson, V. Jo, Luthey-Schulten, Zaida A.

Journal:

Year:

2007

Language:

english

File:

PDF, 1.12 MB

english, 2007

61

Cytochrome c 2 Exit Strategy: Dissociation Studies and Evolutionary Implications

Pogorelov, Taras V., Autenrieth, Felix, Roberts, Elijah, Luthey-Schulten, Zaida A.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 2.12 MB

english, 2007

62

Toward an outline of the topography of a realistic protein-folding funnel.

Onuchic, J. N., Wolynes, P. G., Luthey-Schulten, Z., Socci, N. D.

Journal:

Proceedings of the National Academy of Sciences

Year:

1995

Language:

english

File:

PDF, 1.33 MB

english, 1995

63

Assembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go̅ Simulations

Chen, Ke, Eargle, John, Lai, Jonathan, Kim, Hajin, Abeysirigunawardena, Sanjaya, Mayerle, Megan, Woodson, Sarah, Ha, Taekjip, Luthey-Schulten, Zaida

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 5.18 MB

english, 2012

64

Barriers to Forced Transitions in Polysaccharides

O'Donoghu, Patrick, Luthey-Schulten, Zaida Ann

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 139 KB

english, 2000

65

From The Cover: Water in protein structure prediction

Papoian, G. A., Ulander, J., Eastwood, M. P., Luthey-Schulten, Z., Wolynes, P. G.

Journal:

Proceedings of the National Academy of Sciences

Year:

2004

Language:

english

File:

PDF, 864 KB

english, 2004

66

[IEEE Distributed Processing (IPDPS) - Rome, Italy (2009.05.23-2009.05.29)] 2009 IEEE International Symposium on Parallel & Distributed Processing - Long time-scale simulations of in vivo diffusion using GPU hardware

Roberts, Elijah, Stone, John E., Sepulveda, Leonardo, Hwu, Wen-Mei W., Luthey-Schulten, Zaida

Year:

2009

Language:

english

File:

PDF, 518 KB

english, 2009

67

Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement

Butler, Thomas, Goldenfeld, Nigel, Mathew, Damien, Luthey-Schulten, Zaida

Journal:

Physical Review E

Year:

2009

Language:

english

File:

PDF, 95 KB

english, 2009

68

Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach

Eastwood, Michael P., Hardin, Corey, Luthey-Schulten, Zaida, Wolynes, Peter G.

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 397 KB

english, 2003

69

Extrinsic Noise Driven Phenotype Switching in a Self-Regulating Gene

Assaf, Michael, Roberts, Elijah, Luthey-Schulten, Zaida, Goldenfeld, Nigel

Journal:

Physical Review Letters

Year:

2013

Language:

english

File:

PDF, 587 KB

english, 2013

70

Determining the Stability of Genetic Switches: Explicitly Accounting for mRNA Noise

Assaf, Michael, Roberts, Elijah, Luthey-Schulten, Zaida

Journal:

Physical Review Letters

Year:

2011

Language:

english

File:

PDF, 551 KB

english, 2011

71

Is the olfactory receptor a metalloprotein?

Wang, J., Luthey-Schulten, Z. A., Suslick, K. S.

Journal:

Proceedings of the National Academy of Sciences

Year:

2003

Language:

english

File:

PDF, 483 KB

english, 2003

72

Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer

Takada, Shoji, Luthey-Schulten, Zaida, Wolynes, Peter G.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 887 KB

english, 1999

73

[IEEE Comput. Soc. Press Proceedings of the Twenty-Seventh Annual Hawaii International Conference on System Sciences - Wailea, HI, USA (1994.01.4-1994.01.7)] Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-94 - A Bayesian approach to sequence alignment algorithms for protein structure recognition

Goldstein,, Luthey-Schulten,, Wolynes,

Year:

1994

Language:

english

File:

PDF, 798 KB

english, 1994

74

Whole Cell Modeling: From Single Cells to Colonies

Cole, John A., Luthey-Schulten, Zaida

Journal:

Israel Journal of Chemistry

Year:

2014

Language:

english

File:

PDF, 2.02 MB

english, 2014

75

Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites

Li Li, Michal T. Boniecki, Jacob D. Jaffe, Brian S. Imai, Peter M. Yau, Zaida A. Luthey-Schulten and Susan A. Martinis

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.78 MB

english, 2011

76

Protein tertiary structure recognition using optimized Hamiltonians with local interactions.

Goldstein, R. A., Luthey-Schulten, Z. A., Wolynes, P. G.

Journal:

Proceedings of the National Academy of Sciences

Year:

1992

Language:

english

File:

PDF, 1.03 MB

english, 1992

77

Native Conformational Dynamics of the Spliceosomal U1A Protein

Guzman, Irisbel, Ghaemi, Zhaleh, Baranger, Anne, Luthey-Schulten, Zaida, Gruebele, Martin

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 3.40 MB

english, 2015

78

Electrostatic Interaction Effects on the Binding of Spliceosomal U1A Protein-SL2 RNA Hairpin

Ghaemi, Zhaleh, Guzman, Irisbel, Gruebele, Martin, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 39 KB

english, 2015

79

Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer

Luthey-Schulten, Zaida, Ramirez, Benjamin E., Wolynes, Peter G.

Journal:

Journal of Physical Chemistry

Year:

1995

Language:

english

File:

PDF, 1.06 MB

english, 1995

80

Corrigendum: DNA looping increases the range of bistability in a stochastic model of the lac genetic switch (2013 Phys. Biol. 10 026002)

Earnest, Tyler M, Roberts, Elijah, Assaf, Michael, Dahmen, Karin, Luthey-Schulten, Zaida

Journal:

Physical Biology

Year:

2014

Language:

english

File:

PDF, 63 KB

english, 2014

81

Developing an energy landscape for the novel function of a ( / )8 barrel: Ammonia conduction through HisF

Amaro, R., Tajkhorshid, E., Luthey-Schulten, Z.

Journal:

Proceedings of the National Academy of Sciences

Year:

2003

Language:

english

File:

PDF, 288 KB

english, 2003

82

Associative memory Hamiltonians for structure prediction without homology: Alpha-helical proteins

Hardin, C., Eastwood, M. P., Luthey-Schulten, Z., Wolynes, P. G.

Journal:

Proceedings of the National Academy of Sciences

Year:

2000

Language:

english

File:

PDF, 543 KB

english, 2000

83

Evolutionary profiles from the QR factorization of multiple sequence alignments

Sethi, A., O'Donoghue, P., Luthey-Schulten, Z.

Journal:

Proceedings of the National Academy of Sciences

Year:

2005

Language:

english

File:

PDF, 637 KB

english, 2005

84

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population

Labhsetwar, Piyush, Cole, John Andrew, Roberts, Elijah, Price, Nathan D., Luthey-Schulten, Zaida A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 2.64 MB

english, 2013

85

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Cole, John A, Kohler, Lars, Hedhli, Jamila, Luthey-Schulten, Zaida

Journal:

BMC Systems Biology

Year:

2015

Language:

english

File:

PDF, 1.45 MB

english, 2015

86

Molecular signatures of ribosomal evolution

Roberts, E., Sethi, A., Montoya, J., Woese, C. R., Luthey-Schulten, Z.

Journal:

Proceedings of the National Academy of Sciences

Year:

2008

Language:

english

File:

PDF, 689 KB

english, 2008

87

The evolutionary history of Cys-tRNACys formation

O'Donoghue, P., Sethi, A., Woese, C. R., Luthey-Schulten, Z. A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2005

Language:

english

File:

PDF, 1.77 MB

english, 2005

88

Associative memory Hamiltonians for structure prediction without homology: / proteins

Hardin, C., Eastwood, M. P., Prentiss, M. C., Luthey-Schulten, Z., Wolynes, P. G.

Journal:

Proceedings of the National Academy of Sciences

Year:

2003

Language:

english

File:

PDF, 263 KB

english, 2003

89

On the Evolution of Structure in Aminoacyl-tRNA Synthetases

O'Donoghue, P., Luthey-Schulten, Z.

Journal:

Microbiology and Molecular Biology Reviews

Year:

2003

Language:

english

File:

PDF, 4.00 MB

english, 2003

90

DNA looping increases the range of bistability in a stochastic model of the lac genetic switch

Earnest, Tyler M, Roberts, Elijah, Assaf, Michael, Dahmen, Karin, Luthey-Schulten, Zaida

Journal:

Physical Biology

Year:

2013

Language:

english

File:

PDF, 1.88 MB

english, 2013

91

Multiple Alignment of protein structures and sequences for VMD

Eargle, J., Wright, D., Luthey-Schulten, Z.

Journal:

Year:

2006

Language:

english

File:

PDF, 216 KB

english, 2006

92

Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites

Li, L., Boniecki, M. T., Jaffe, J. D., Imai, B. S., Yau, P. M., Luthey-Schulten, Z. A., Martinis, S. A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.94 MB

english, 2011

93

Dynamical networks in tRNA:protein complexes

Sethi, A., Eargle, J., Black, A. A., Luthey-Schulten, Z.

Journal:

Proceedings of the National Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 462 KB

english, 2009

94

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Roberts, Elijah, Magis, Andrew, Ortiz, Julio O., Baumeister, Wolfgang, Luthey-Schulten, Zaida, Csermely, Peter

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.01 MB

english, 2011

95

Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly

Earnest, Tyler M., Lai, Jonathan, Chen, Ke, Hallock, Michael J., Williamson, James R., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 2.06 MB

english, 2015

96

Optimal Protein-Folding Codes from Spin-Glass Theory

Richard A. Goldstein, Zaida A. Luthey-Schulten and Peter G. Wolynes

Journal:

Proceedings of the National Academy of Sciences

Year:

1992

Language:

english

File:

PDF, 1.16 MB

english, 1992

97

Three-Dimensional Model for the Hormone Binding Domains of Steroid Receptors

Richard A. Goldstein, John A. Katzenellenbogen, Zaida A. Luthey-Schulten, Donald A. Seielstad and Peter G. Wolynes

Journal:

Proceedings of the National Academy of Sciences

Year:

1993

Language:

english

File:

PDF, 1.40 MB

english, 1993

98

Effects of DNA replication on mRNA noise

Peterson, Joseph R., Cole, John A., Fei, Jingyi, Ha, Taekjip, Luthey-Schulten, Zaida A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

99

Role of Water in Transient Cytochrome c 2 Docking

Autenrieth, Felix, Tajkhorshid, Emad, Schulten, Klaus, Luthey-Schulten, Zaida

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 1.52 MB

english, 2004

100

Toward an Outline of the Topography of a Realistic Protein-Folding Funnel

J. N. Onuchic, P. G. Wolynes, Z. Luthey-Schulten and N. D. Socci

Journal:

Proceedings of the National Academy of Sciences

Year:

1995

Language:

english

File:

PDF, 377 KB

english, 1995