Luthey-Schulten, Zaida: 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

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

7

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

8

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

9

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

10

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

11

[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

12

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

13

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

14

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

15

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

16

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

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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

31

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

32

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

33

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

34

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

35

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

36

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

37

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

38

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

39

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

40

Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

Peterson, Joseph R., Thor, ShengShee, Kohler, Lars, Kohler, Petra R.A., Metcalf, William W., Luthey-Schulten, Zaida

Journal:

Year:

2016

Language:

english

File:

PDF, 7.85 MB

english, 2016

41

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

42

Integration of Reaction-Diffusion Master Equation and Brownian Dynamics Methodologies to Simulate a Minimal Cell

Earnest, Tyler M., Hallock, Michael J., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 61 KB

2019

43

Dynamical Network Analysis of Protein:RNA Complexes Made Easy

dos Reis Melo, Marcelo Cardoso, Bernardi, Rafael C., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 59 KB

english, 2019

44

Stochastic Analysis Demonstrates the Dual Role of Hfq in Chaperoning E. coli Sugar Shock Response

Bianchi, David M., Brier, Troy A., Poddar, Anustup, Azam, Muhammad S., Vanderpool, Carin K., Ha, Taekjip, Luthey-Schulten, Zaida

Journal:

Frontiers in Molecular Biosciences

Year:

2020

File:

PDF, 2.06 MB

2020

45

Exploring Residue Component Contributions to Dynamical Network Models of Allostery

VanWart, Adam T., Eargle, John, Luthey-Schulten, Zaida, Amaro, Rommie E.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 2.28 MB

english, 2012

46

Capture and Quality Control Mechanisms for Adenosine-5′-triphosphate Binding

Li, Li, Martinis, Susan A., Luthey-Schulten, Zaida

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 4.88 MB

english, 2013

47

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

48

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

49

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

50

Estimation of Relative Protein-RNA Binding Strengths from Fluctuations in the Bound State

Ghaemi, Zhaleh, Guzman, Irisbel, Baek, Jung-un Julia, Gruebele, Martin, Luthey-Schulten, Zaida

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 1.11 MB

english, 2016

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