Z. Luthey-Schulten: search on Z-Library

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1

THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

Onuchic, José Nelson, Luthey-Schulten, Zaida, Wolynes, Peter G.

Journal:

Annual Review of Physical Chemistry

Year:

1997

Language:

english

File:

PDF, 524 KB

english, 1997

2

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

Chen, Ke, Fei, Jingyi, Zhang, Jichuan, Cole, John, Ha, Taekjip, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 37 KB

english, 2013

3

Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism

Zhao, Hanchao, Palencia, Andres, Seiradake, Elena, Ghaemi, Zhaleh, Cusack, Stephen, Luthey-Schulten, Zaida, Martinis, Susan

Journal:

ACS Chemical Biology

Year:

2015

Language:

english

File:

PDF, 1.61 MB

english, 2015

4

Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Thor, ShengShee, Peterson, Joseph R., Luthey-Schulten, Zaida

Journal:

Year:

2017

Language:

english

File:

PDF, 1.99 MB

english, 2017

5

New QMMM Interface to NAMD Probes tRNA Charging Mechanism

Melo, Marcelo C., Bernardi, Rafael C., Schulten, Klaus, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 58 KB

english, 2018

6

Self-consistently optimized statistical mechanical energy functions for sequence structure alignment

K. K. Koretke, Z. Luthey-Schulten, P. G. Wolynes

Journal:

Protein Science

Year:

1996

Language:

english

File:

PDF, 3.96 MB

english, 1996

7

Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach

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

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 416 KB

english, 2002

8

Towards a Computational Model of a Methane Producing Archaeum

Peterson, Joseph R., Labhsetwar, Piyush, Ellermeier, Jeremy R., Kohler, Petra R. A., Jain, Ankur, Ha, Taekjip, Metcalf, William W., Luthey-Schulten, Zaida

Journal:

Year:

2014

Language:

english

File:

PDF, 5.89 MB

english, 2014

9

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

Cassidy, C. Keith, Himes, Benjamin A., Sun, Dapeng, Ma, Jun, Zhao, Gongpu, Parkinson, John S., Stansfeld, Phillip J., Luthey-Schulten, Zaida, Zhang, Peijun

Journal:

Communications Biology

Year:

2020

Language:

english

File:

PDF, 2.40 MB

english, 2020

10

Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study

Damien C. Mathew, Zaida Luthey-Schulten

Journal:

Origins of Life and Evolution of Biospheres

Year:

2010

Language:

english

File:

PDF, 494 KB

english, 2010

11

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

12

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

13

[IEEE 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - Chicago, IL, USA (2016.5.23-2016.5.27)] 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

Stone, John E., Hallock, Michael J., Phillips, James C., Peterson, Joseph R., Luthey-Schulten, Zaida, Schulten, Klaus

Year:

2016

Language:

english

File:

PDF, 1.83 MB

english, 2016

14

A Computational Human Whole-Cell Model Reveals the Effects of Spatial Organization on RNA Splicing

Ghaemi, Zhaleh, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 45 KB

english, 2019

15

Optimal protein-folding codes from spin-glass theory.

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

Journal:

Proceedings of the National Academy of Sciences

Year:

1992

Language:

english

File:

PDF, 1.32 MB

english, 1992

16

Modelling the Nucleotide Metabolic Network of a Genetically Minimal Cell

Brier, Troy A., Bianchi, David, Thornburg, Zane R., dos Reis Melo, Marcelo Cardoso, Breuer, Marian, Wise, Kim S., Smith, Hamilton O., Hutchison, Clyde A., Glass, John I., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 69 KB

2020

17

Molecular Mechanism of Conformational Switching that Regulates Helicase Function

Ma, Wen, Carney, Sean, Chemla, Yann R., Luthey-Schulten, Zaida, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 71 KB

2020

18

Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

Ke Chen, Elijah Roberts, Zaida Luthey-Schulten

Journal:

BMC Evolutionary Biology

Year:

2009

Language:

english

File:

PDF, 2.23 MB

english, 2009

19

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

20

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

21

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

Earnest, Tyler M., Chen, Ke, Lai, Jonathan, Luthey-Schulten, Zan

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

22

Classical force field parameters for the heme prosthetic group of cytochrome c

Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zaida Luthey-Schulten

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 456 KB

english, 2004

23

Exit Strategies for Charged tRNA from GluRS

Alexis Black Pyrkosz, John Eargle, Anurag Sethi, Zaida Luthey-Schulten

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.70 MB

english, 2010

24

The Role of L1 Stalk–tRNA Interaction in the Ribosome Elongation Cycle

Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha, Zaida Luthey-Schulten, Klaus Schulten

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.76 MB

english, 2010

25

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

26

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

27

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

28

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

29

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

30

Whole-Cell Simulations of mRNA Production in Eukaryotic Cell Models

Ghaemi, Zhaleh, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

31

Molecular dynamics simulations of substrate channeling through an α–β barrel protein

Rommie Amaro, Zaida Luthey-Schulten

Journal:

Chemical Physics

Year:

2004

Language:

english

File:

PDF, 925 KB

english, 2004

32

Gas-phase methanol solvation of Cs+ : Vibrational spectroscopy and Monte Carlo simulation

Draves, Jeffrey A., Luthey-Schulten, Zaida, Liu, Wen-Long, Lisy, James M.

Journal:

The Journal of Chemical Physics

Year:

1990

Language:

english

File:

PDF, 1.27 MB

english, 1990

33

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

34

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

35

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

36

Three-dimensional model for the hormone binding domains of steroid receptors.

Goldstein, R. A., Katzenellenbogen, J. A., Luthey-Schulten, Z. A., Seielstad, D. A., Wolynes, P. G.

Journal:

Proceedings of the National Academy of Sciences

Year:

1993

Language:

english

File:

PDF, 1.53 MB

english, 1993

37

Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain

Burt, Alister, Cassidy, C. Keith, Ames, Peter, Bacia-Verloop, Maria, Baulard, Megghane, Huard, Karine, Luthey-Schulten, Zaida, Desfosses, Ambroise, Stansfeld, Phillip J., Margolin, William, Parkinson,

Journal:

Nature Communications

Year:

2020

File:

PDF, 4.30 MB

2020

38

Fast-folding eriments and the topography of protein folding energy landscapes

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

Journal:

Chemistry & Biology

Year:

1996

Language:

english

File:

PDF, 3.13 MB

english, 1996

39

MultiSeq: unifying sequence and structure data for evolutionary analysis

Elijah Roberts, John Eargle, Dan Wright, Zaida Luthey-Schulten

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 707 KB

english, 2006

40

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

41

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

42

Simulating Biological Processes: Stochastic Physics from Whole Cells to Colonies

Earnest, Tyler, Cole, John Andrew, Luthey-Schulten, Zaida

Journal:

Reports on Progress in Physics

Year:

2018

Language:

english

File:

PDF, 5.61 MB

english, 2018

43

On the Physical Basis of the Amino Acid Polar Requirement

Damien C. Mathew, Zaida Luthey-Schulten

Journal:

Journal of Molecular Evolution

Year:

2008

Language:

english

File:

PDF, 566 KB

english, 2008

44

Heterogenity in Protein Copy Numbers induces Metabolic Variability in Modeled E. coli Populations

Labhsetwar, Piyush, Cole, John, Roberts, Elijah, Price, Nathan, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 36 KB

english, 2013

45

Modeling Metabolic Variability in Methanosarcina Acetivorans

Peterson, Joseph R., Labhsetwar, Piyush, Kohler, Petra, Ellermeier, Jeremy, Metcalf, William, Jain, Ankur, Ha, Taekjip, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 38 KB

english, 2014

46

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

47

The foldon universe: a survey of structural similarity and self-recognition of independently folding units

Anna R Panchenko, Zaida Luthey-Schulten, Ronald Cole, Peter G Wolynes

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 567 KB

english, 1997

48

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

49

Spatial Organization of Ribosome Biogenesis of Escherichia Coli

Nguyen, Cac T., Ngo, Thuy, Park, Seongjin, Cox, Khan, Ha, Taekjip, Luthey-Schulten, Zaida A., Kuhlman, Thomas E.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 43 KB

english, 2015

50

CryoEM-based hybrid modeling approaches for structure determination

Cassidy, C Keith, Himes, Benjamin A, Luthey-Schulten, Zaida, Zhang, Peijun

Journal:

Current Opinion in Microbiology

Year:

2018

Language:

english

File:

PDF, 2.31 MB

english, 2018

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