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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

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

4

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

5

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

6

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

7

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

8

Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus

P. Haney, J. Konisky, K. K. Koretke, Z. Luthey-Schulten, P. G. Wolynes

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 333 KB

english, 1997

9

Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides

Corey Hardin, Zaida Luthey-Schulten, Peter G. Wolynes

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 214 KB

english, 1999

10

Folding funnels: The key to robust protein structure prediction

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

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 998 KB

english, 2002

11

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

12

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

13

Visualizing the dual space of biological molecules

John Eargle, Zaida Luthey-Schulten

Journal:

Computational Biology and Chemistry

Year:

2006

Language:

english

File:

PDF, 519 KB

english, 2006

14

Foldons as independently folding units of proteins

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

Journal:

Physica D: Nonlinear Phenomena

Year:

1997

Language:

english

File:

PDF, 268 KB

english, 1997

15

Optimizing physical energy functions for protein folding

Yoshimi Fujitsuka, Shoji Takada, Zaida A. Luthey-Schulten, Peter G. Wolynes

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 348 KB

english, 2004

16

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

17

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

18

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

19

Experimental and computational determination of tRNA dynamics

Rebecca W. Alexander, John Eargle, Zaida Luthey-Schulten

Journal:

Year:

2010

Language:

english

File:

PDF, 1.23 MB

english, 2010

20

Ab initio protein structure prediction

Corey Hardin, Taras V Pogorelov, Zaida Luthey-Schulten

Journal:

Current Opinion in Structural Biology

Year:

2002

Language:

english

File:

PDF, 77 KB

english, 2002

21

Protein folding funnels: the nature of the transition state ensemble

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

Journal:

Folding and Design

Year:

1996

Language:

english

File:

PDF, 321 KB

english, 1996

22

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

23

Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation

Elijah Roberts, John E. Stone, Zaida Luthey-Schulten

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 1.11 MB

english, 2012

24

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

25

On the Structure of hisH: Protein Structure Prediction in the Context of Structural and Functional Genomics

P. O'Donoghue, R.E. Amaro, Z. Luthey-Schulten

Journal:

Journal of Structural Biology

Year:

2001

Language:

english

File:

PDF, 1.65 MB

english, 2001

26

Evolutionary Profiles Derived from the QR Factorization of Multiple Structural Alignments Gives an Economy of Information

Patrick O'Donoghue, Zaida Luthey-Schulten

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 1004 KB

english, 2005

27

Dynamics of Recognition between tRNA and Elongation Factor Tu

John Eargle, Alexis A. Black, Anurag Sethi, Leonardo G. Trabuco, Zaida Luthey-Schulten

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 2.90 MB

english, 2008

28

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

29

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

30

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

31

NetworkView: 3D display and analysis of protein{middle dot}RNA interaction networks

Eargle, J., Luthey-Schulten, Z.

Journal:

Year:

2012

Language:

english

File:

PDF, 171 KB

english, 2012

32

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

33

Functional Role of Ribosomal Signatures

Chen, Ke, Eargle, John, Sarkar, Krishnarjun, Gruebele, Martin, Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 748 KB

english, 2010

34

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

35

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

36

Structural Elements in IGP Synthase Exclude Water to Optimize Ammonia Transfer

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

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 1.47 MB

english, 2005

37

Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens

Li, L., Palencia, A., Lukk, T., Li, Z., Luthey-Schulten, Z. A., Cusack, S., Martinis, S. A., Boniecki, M. T.

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 1.12 MB

english, 2013

38

Variations in the Fast Folding Rates of the λ-Repressor: A Hybrid Molecular Dynamics Study

Pogorelov, Taras V., Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 271 KB

english, 2004

39

Reaction Coupling through Interdomain Contacts in Imidazole Glycerol Phosphate Synthase †

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

Journal:

Year:

2005

Language:

english

File:

PDF, 765 KB

english, 2005

40

How R-Proteins Stabilize the R-RNA during Early Stages of Bacterial Ribosome Biogenesis

Lai, Jonathan, Chen, Ke, Kim, Hajin, Ha, Taejkip, Woodson, Sarah, Luthey-Schulten, Zan

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 41 KB

english, 2013

41

Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit

Lai, Jonathan, Chen, Ke, Luthey-Schulten, Zaida

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 2.23 MB

english, 2013

42

Protein-guided RNA dynamics during early ribosome assembly

Kim, Hajin, Abeysirigunawarden, Sanjaya C., Chen, Ke, Mayerle, Megan, Ragunathan, Kaushik, Luthey-Schulten, Zaida, Ha, Taekjip, Woodson, Sarah A.

Journal:

Year:

2014

Language:

english

File:

PDF, 3.74 MB

english, 2014

43

Single Molecule Views of the Ribosome Assembly

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

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

44

Editorial Board

Roberts, Elijah, Magis, Andrew T., Luthey-Schulten, Zan

Journal:

Journal of Dairy Science

Year:

1981

Language:

english

File:

PDF, 92 KB

english, 1981

45

The Effects of Spatial Heterogeneity and in vivo Crowding on the Lac Genetic Circuit

Roberts, Elijah, Magis, Andrew T., Luthey-Schulten, Zan

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 38 KB

english, 2010

46

Stochastic Simulations of Cellular Processes: From Single Cells to Colonies

Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 38 KB

english, 2014

47

Stochastic Simulations of Cellular Processes in Bacteria

Luthey-Schulten, Zaida

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 37 KB

english, 2013

48

Elucidating Metabolic Variability in Isogenic Microbial Populations Arising due to Noise in Protein Expression

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

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 47 KB

english, 2014

49

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

50

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