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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

Knotting pathways in proteins

Sułkowska, Joanna I., Noel, Jeffrey K., Ramírez‑Sarmiento, César A., Rawdon, Eric J., Millett, Kenneth C., Onuchic, José N.

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 354 KB

english, 2013

3

Understanding protein folding with energy landscape theory Part II: Quantitative aspects

Plotkin, Steven S., Onuchic, José N.

Journal:

Quarterly Reviews of Biophysics

Year:

2002

Language:

english

File:

PDF, 1.95 MB

english, 2002

4

Foldable structures and the natural design of pollen grains

Eleni Katifori, Silas Alben, Enrique Cerda, David R. Nelson, Jacques Dumais and José N. Onuchic

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.42 MB

english, 2010

5

The physics of bacterial decision making

Ben-Jacob, Eshel, Lu, Mingyang, Schultz, Daniel, Onuchic, Jose' N.

Journal:

Frontiers in Cellular and Infection Microbiology

Year:

2014

Language:

english

File:

PDF, 5.74 MB

english, 2014

6

RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere

Lammert, Heiko, Wang, Ailun, Mohanty, Udayan, Onuchic, José N.

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 2.41 MB

english, 2018

7

Electron tunneling pathways in proteins: influences on the transfer rate

David N. Beratan, José Nelson Onuchic

Journal:

Photosynthesis Research

Year:

1989

Language:

english

File:

PDF, 1.22 MB

english, 1989

8

Protein Oligomerization Through Domain Swapping: Role of Inter-molecular Interactions and Protein Concentration

Sichun Yang, Herbert Levine, José N. Onuchic

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 712 KB

english, 2005

9

Folding Time Predictions from All-atom Replica Exchange Simulations

Sichun Yang, José N. Onuchic, Angel E. García, Herbert Levine

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 670 KB

english, 2007

10

Understanding protein folding with energy landscape theory Part I: Basic concepts

Plotkin, Steven S., Onuchic, José N.

Journal:

Quarterly Reviews of Biophysics

Year:

2002

Language:

english

File:

PDF, 1.09 MB

english, 2002

11

[Advances in Protein Chemistry] Protein folding mechanisms Volume 53 || The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios

Nelson Onuchic, José

Year:

2000

Language:

english

File:

PDF, 4.38 MB

english, 2000

12

Effective stochastic dynamics on a protein folding energy landscape

Yang, Sichun, Onuchic, José N., Levine, Herbert

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 936 KB

english, 2006

13

Intercellular Stress Reconstitution from Traction Force Data

Zimmermann, Juliane, Hayes, Ryan L., Basan, Markus, Onuchic, José N., Rappel, Wouter-Jan, Levine, Herbert

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.06 MB

english, 2014

14

Slipknotting upon native-like loop formation in a trefoil knot protein

Jeffrey K. Noel, Joanna I. Sułkowska and José N. Onuchic

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.81 MB

english, 2010

15

Connecting Thermal and Mechanical Protein (Un)folding Landscapes

Sun, Li, Noel, Jeffrey K., Sulkowska, Joanna I., Levine, Herbert, Onuchic, José N.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.42 MB

english, 2014

16

Hyper telomere recombination accelerates replicative senescence and may promote premature aging

R. Tanner Hagelstrom, Krastan B. Blagoev, Laura J. Niedernhofer, Edwin H. Goodwin, Susan M. Bailey and José N. Onuchic

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.44 MB

english, 2010

17

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

Hayes, Ryan L., Noel, Jeffrey K., Mandic, Ana, Whitford, Paul C., Sanbonmatsu, Karissa Y., Mohanty, Udayan, Onuchic, José N.

Journal:

Physical Review Letters

Year:

2015

Language:

english

File:

PDF, 240 KB

english, 2015

18

Toward understanding cancer stem cell heterogeneity in the tumor microenvironment

Bocci, Federico, Gearhart-Serna, Larisa, Boareto, Marcelo, Ribeiro, Mariana, Ben-Jacob, Eshel, Devi, Gayathri R., Levine, Herbert, Onuchic, José Nelson, Jolly, Mohit Kumar

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 1.80 MB

english, 2018

19

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

Roy, Susmita, Hennelly, Scott P, Lammert, Heiko, Onuchic, José N, Sanbonmatsu, Karissa Y

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 2.99 MB

english, 2019

20

Protein folding mechanisms and the multidimensional folding funnel

Nicholas D. Socci, José Nelson Onuchic, Peter G. Wolynes

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 475 KB

english, 1998

21

The folding funnel landscape for the peptide met-enkephalin

Ulrich H.E. Hansmann, Yuko Okamoto, Jose N. Onuchic

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 477 KB

english, 1999

22

Equilibrium unfolding of the poly(glutamic acid)20 helix

John M. Finke, Patricia A. Jennings, Jennifer C. Lee, José N. Onuchic, Jay R. Winkler

Journal:

Year:

2007

Language:

english

File:

PDF, 609 KB

english, 2007

23

Effective two-state systems in bridge-mediated electron transfer. A Green function analysis

Spiros S. Skourtis, José Nelson Onuchic

Journal:

Chemical Physics Letters

Year:

1993

Language:

english

File:

PDF, 532 KB

english, 1993

24

The two-state reduction for electron and hole transfer in bridge-mediated electron-transfer reactions

Spiros S. Skourtis, David N. Beratan, José Nelson Onuchic

Journal:

Chemical Physics

Year:

1993

Language:

english

File:

PDF, 1.79 MB

english, 1993

25

Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions

José Nelson Onuchic, Jin Wang, Peter G. Wolynes

Journal:

Chemical Physics

Year:

1999

Language:

english

File:

PDF, 172 KB

english, 1999

26

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu, José N. Onuchic

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 757 KB

english, 2009

27

Robustness and generalization of structure-based models for protein folding and function

Heiko Lammert, Alexander Schug, José N. Onuchic

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 767 KB

english, 2009

28

The role of atomic level steric effects and attractive forces in protein folding

Heiko Lammert, Peter G. Wolynes, José N. Onuchic

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

29

Funnels, pathways, and the energy landscape of protein folding: A synthesis

Joseph D. Bryngelson, José Nelson Onuchic, Nicholas D. Socci, Peter G. Wolynes

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1995

Language:

english

File:

PDF, 2.98 MB

english, 1995

30

Quantum and classical dynamics in biochemical reactions

William Bialek, William J. Bruno, Julian Joseph, José Nelson Onuchic

Journal:

Photosynthesis Research

Year:

1984

Language:

english

File:

PDF, 1.08 MB

english, 1984

31

The energy landscape for protein folding and possible connections to function

Margaret S. Cheung, Leslie L. Chavez, José N. Onuchic

Journal:

Year:

2004

Language:

english

File:

PDF, 515 KB

english, 2004

32

Nonlinear susceptibilities of finite conjugated organic polymers

Beratan, David N., Onuchic, Jose Nelson., Perry, Joseph W.

Journal:

Journal of Physical Chemistry

Year:

1987

Language:

english

File:

PDF, 394 KB

english, 1987

33

Electronic shift register memory based on molecular electron-transfer reactions

Hopfield, J. J., Onuchic, Jose Nelson, Beratan, David N.

Journal:

Journal of Physical Chemistry

Year:

1989

Language:

english

File:

PDF, 1.12 MB

english, 1989

34

Biomolecular dynamics: order–disorder transitions and energy landscapes

Whitford, Paul C, Sanbonmatsu, Karissa Y, Onuchic, José N

Journal:

Reports on Progress in Physics

Year:

2012

Language:

english

File:

PDF, 2.61 MB

english, 2012

35

Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways

Jesse P. Singh, Paul C. Whitford, N. R. Hayre, José Onuchic, Daniel L. Cox

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.24 MB

english, 2012

36

Theory of protein folding

José Nelson Onuchic, Peter G Wolynes

Journal:

Current Opinion in Structural Biology

Year:

2004

Language:

english

File:

PDF, 269 KB

english, 2004

37

Folding a Protein in the Computer: Reality or Hope?

Angel E. Garcia, José N. Onuchic

Journal:

Year:

2005

Language:

english

File:

PDF, 45 KB

english, 2005

38

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

39

Redox redux

Beratan, David N., Onuchic, José N.

Journal:

Physical Chemistry Chemical Physics

Year:

2012

Language:

english

File:

PDF, 131 KB

english, 2012

40

Fly-Casting in Protein−DNA Binding: Frustration between Protein Folding and Electrostatics Facilitates Target Recognition

Onuchic, José N., Levy, Yaakov, Wolynes, Peter G.

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 147 KB

english, 2007

41

Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? an investigation for small globular proteins

Cecilia Clementi, Hugh Nymeyer, José Nelson Onuchic

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 1024 KB

english, 2000

42

Prediction of folding mechanism for circular-permuted proteins

Cecilia Clementi, Patricia A. Jennings, José N. Onuchic

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 720 KB

english, 2001

43

From protein folding to protein function and biomolecular binding by energy landscape theory

Alexander Schug, José N Onuchic

Journal:

Current Opinion in Pharmacology

Year:

2010

Language:

english

File:

PDF, 431 KB

english, 2010

44

Gatekeepers in the Ribosomal Protein S6: Thermodynamics, Kinetics, and Folding Pathways Revealed by a Minimalist Protein Model

Antitsa D. Stoycheva, Charles L. Brooks III, José N. Onuchic

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 886 KB

english, 2004

45

The Folding and Dimerization of HIV-1 Protease: Evidence for a Stable Monomer from Simulations

Yaakov Levy, Amedeo Caflisch, Jose N. Onuchic, Peter G. Wolynes

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.04 MB

english, 2004

46

Dynamic Coupling Between the SH2 Domain and Active Site of the COOH Terminal Src Kinase, Csk

Lilly Wong, Scot Lieser, Barbara Chie-Leon, Osamu Miyashita, Brandon Aubol, Jennifer Shaffer, Josè N. Onuchic, Patricia A. Jennings, Virgil L. Woods Jr, Joseph A. Adams

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 543 KB

english, 2004

47

A Survey of Flexible Protein Binding Mechanisms and their Transition States Using Native Topology Based Energy Landscapes

Yaakov Levy, Samuel S. Cho, José N. Onuchic, Peter G. Wolynes

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 2.19 MB

english, 2005

48

The Native Energy Landscape for Interleukin-1β. Modulation of the Population Ensemble through Native-state Topology

Melinda Roy, Leslie L. Chavez, John M. Finke, David K. Heidary, José N. Onuchic, Patricia A. Jennings

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 601 KB

english, 2005

49

Coupled Motions in the SH2 and Kinase Domains of Csk Control Src Phosphorylation

Lilly Wong, Scot A. Lieser, Osamu Miyashita, Meghan Miller, Kjetil Tasken, Josè N. Onuchic, Joseph A. Adams, Virgil L. Woods Jr, Patricia A. Jennings

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 493 KB

english, 2005

50

Topological Frustration and the Folding of Interleukin-1β

Shachi Gosavi, Leslie L. Chavez, Patricia A. Jennings, José N. Onuchic

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 1.20 MB

english, 2006

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