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

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Items 301–400 of 1,005

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   Cristian Micheletti, Jayanth R. Banavar, Amos Maritan, Flavio Seno · 1999 · Physical Review Letters
2. Biomolecular dynamics: order–disorder transitions and energy landscapes
   Paul C. Whitford, Karissa Y. Sanbonmatsu, José N. Onuchic · 2012 · Reports on Progress in Physics
3. A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling
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6. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding
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8. Laser Temperature Jump Induced Protein Refolding
   Martin Gruebele, Jobiah J. Sabelko, Richard M. Ballew, John Ervin · 1998 · Accounts of Chemical Research
9. The sequences of small proteins are not extensively optimized for rapid folding by natural selection
   David E. Kim, Hongdi Gu, David A. Baker · 1998 · Proceedings of the National Academy of Sciences
10. Non-Markovian modeling of protein folding
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11. Downhill protein folding: evolution meets physics
    Martin Gruebele · 2005 · Comptes Rendus Biologies
12. A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules
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13. Protein folding transition path times from single molecule FRET
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    M. Apaydın, D. Brutlag, Carlos Guestrin, David Hsu, J. Latombe, Chris Varma · 2002 · Annual International Conference on Research in Computational Molecular Biology
15. A designed four helix bundle protein with native-like structure
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16. Structural relaxation in Morse clusters: Energy landscapes
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17. Protein Folding Kinetics: Barrier Effects in Chemical and Thermal Denaturation Experiments
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18. Evidence for an unfolding and refolding pathway in cytochrome c
    Yujia Xu, Leland C. Mayne, S. Walter Englander · 1998 · Nature Structural Biology
19. Factors governing the foldability of proteins
    Dmitri K. Klimov, Dave Thirumalai · 1996 · Proteins Structure Function and Bioinformatics
20. Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature
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21. Single-molecule spectroscopy of protein folding in a chaperonin cage
    Hagen Hofmann, Frank Hillger, Shawn H. Pfeil, Armin Hoffmann, Daniel Streich, Dominik Haenni, Daniel Nettels, Everett A. Lipman, Benjamin Schuler · 2010 · Proceedings of the National Academy of Sciences
22. Dry molten globule intermediates and the mechanism of protein unfolding
    Robert L. Baldwin, Carl Frieden, George D. Rose · 2010 · Proteins Structure Function and Bioinformatics
23. Effect of Hierarchical Cluster Formation on the Viscosity of Concentrated Monoclonal Antibody Formulations Studied by Neutron Scattering
    P. Douglas Godfrin, Isidro E. Zarraga, Jonathan Zarzar, Lionel Porcar, Péter Falus, Norman J. Wagner, Yun Liu · 2015 · The Journal of Physical Chemistry B
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    Aleksandr V. Mikhonin, Nataliya S. Myshakina, Sergei V. Bykov, Sanford A. Asher · 2005 · Journal of the American Chemical Society
25. β-Hairpin and β-sheet formation in designed linear peptides
    Marina Ramı́rez-Alvarado, Tanja Kortemme, Francisco J. Blanco, Luis Serrano · 1999 · Bioorganic & Medicinal Chemistry
26. Rate of Intrachain Diffusion of Unfolded Cytochrome c
    Stephen J. Hagen, James Hofrichter, William A. Eaton · 1997 · The Journal of Physical Chemistry B
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    Wenfei Li, Jian Zhang, Jun Wang, Wei Wang · 2007 · Journal of the American Chemical Society
28. Fast events in protein folding
    William A. Eaton, Peggy A Thompson, Chi-Kin Chan, Stephen J Hage, James Hofrichter · 1996 · Structure
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    Zhe Wang, Huiyong Sun, Chao Shen, Xueping Hu, Junbo Gao, Dan Li, Dongsheng Cao, Tingjun Hou · 2020 · Physical Chemistry Chemical Physics
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    Dominique Bicout, Attila Szabó · 2000 · Protein Science
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    Victor Abkevich, Eugene I. Shakhnovich · 2000 · Journal of Molecular Biology
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    B. Doliwa, Andreas Heuer · 2003 · Physical Review Letters
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    J. Raúl Grigera, Andrés N. McCarthy · 2010 · Biophysical Journal
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    Ivano Tavernelli, Simona Cotesta, Ernesto E. Di Iorio · 2003 · Biophysical Journal
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    Andrew P. Latham, Bin Zhang · 2019 · Journal of Chemical Theory and Computation
38. Conformational Transitions in Adenylate Kinase
    Paul C. Whitford, Shachi Gosavi, José N. Onuchic · 2007 · Journal of Biological Chemistry
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    Haipeng Gong, Daniel G. Isom, Rajgopal Srinivasan, George D. Rose · 2003 · Journal of Molecular Biology
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    B. Morrow, G. Payne, Jana Shen · 2015 · Journal of the American Chemical Society
41. Exploring protein-folding ensembles: A variable-barrier model for the analysis of equilibrium unfolding experiments
    Víctor Muñoz, José M. Sánchez‐Ruiz · 2004 · Proceedings of the National Academy of Sciences
42. Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration
    Hugh Nymeyer, Nicholas D. Socci, José N. Onuchic · 2000 · Proceedings of the National Academy of Sciences
43. Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9 1 1Edited by P. E. Wright
    Brian A. Kuhlman, Donna L. Luisi, Philip A. Evans, Daniel P. Raleigh · 1998 · Journal of Molecular Biology
44. Physics of Proteins
    Jayanth R. Banavar, Amos Maritan · 2007 · Annual Review of Biophysics and Biomolecular Structure
45. Thermodynamics of protein folding: A statistical mechanical study of a small all-β protein
    Zhuyan Guo, Charles L. Brooks · 1997 · Biopolymers
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    Sahand Hormoz, Michael P. Brenner · 2011 · Proceedings of the National Academy of Sciences
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    M. Bernetti, A. Cavalli, L. Mollica · 2017 · MedChemComm
48. Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures
    Nancy M. Amato, Ken A. Dill, Guang Song · 2003 · Journal of Computational Biology
49. Direct measurement of protein energy landscape roughness
    Reinat Nevo, Vlad Brumfeld, Ruti Kapon, Peter Hinterdorfer, Ziv Reich · 2005 · EMBO Reports
50. Predictive energy landscapes for protein–protein association
    Weihua Zheng, Nicholas P. Schafer, Aram Davtyan, Garegin A. Papoian, Peter Guy Wolynes · 2012 · Proceedings of the National Academy of Sciences
51. Intrinsically Disordered Energy Landscapes
    Yassmine Chebaro, Andrew J. Ballard, Debayan Chakraborty, David J. Wales · 2015 · Scientific Reports
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    Suman Das, Adam J. Eisen, Yi‐Hsuan Lin, Hue Sun Chan · 2018 · The Journal of Physical Chemistry B
53. Mathematical Analysis of Coupled Parallel Simulations
    Michael R. Shirts, Vijay S. Pande · 2001 · Physical Review Letters
54. Variational Theory for Site Resolved Protein Folding Free Energy Surfaces
    John J. Portman, Shoji Takada, Peter Guy Wolynes · 1998 · Physical Review Letters
55. Physics of viral dynamics
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    M. Vogel, B. Doliwa, Andreas Heuer, Sharon C. Glotzer · 2004 · The Journal of Chemical Physics
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    Mark A. Miller, David J. Wales · 1999 · The Journal of Chemical Physics
58. Unified Description of Urea Denaturation: Backbone and Side Chains Contribute Equally in the Transfer Model
    Beate Moeser, Dominik Horinek · 2013 · The Journal of Physical Chemistry B
59. Flexible selection of the solute region in replica exchange with solute tempering: Application to protein-folding simulations
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60. Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations
    Andrea Soranno, Andrea Holla, Fabian Dingfelder, Daniel Nettels, Dmitrii E. Makarov, Benjamin Schuler · 2017 · Proceedings of the National Academy of Sciences
61. On potential energy surfaces and relaxation to the global minimum
    Jonathan P. K. Doye, David J. Wales · 1996 · The Journal of Chemical Physics
62. Dynamics of Lysozyme Structure Network: Probing the Process of Unfolding
    Amit Ghosh, K. V. Brinda, Saraswathi Vishveshwara · 2007 · Biophysical Journal
63. Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model
    Leonid A. Mirny, Victor Abkevich, Eugene I. Shakhnovich · 1996 · Folding and Design
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    Andrew J. Ballard, Ritankar Das, Stefano Martiniani, Dhagash B. Mehta, Levent Sagun, Jacob D. Stevenson, David J. Wales · 2017 · Physical Chemistry Chemical Physics
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    Ji‐Eun Lee, Jason C. Sang, Margarida Rodrigues, Alexander R. Carr, Mathew H. Horrocks, Suman De, Marie N. Bongiovanni, Patrick Flagmeier, Christopher Martin Dobson, David J. Wales et al. · 2018 · Nano Letters
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    H. Jane Dyson, Peter E. Wright · 2005 · Methods in enzymology on CD-ROM/Methods in enzymology
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    Steven Samuel Plotkin, José N. Onuchic · 2002 · Quarterly Reviews of Biophysics
68. Protein folding and its links with human disease
    Alan Berry · 2001 · Biochemical Society Symposia
69. Ultra-fast Barrier-limited Folding in the Peripheral Subunit-binding Domain Family
    Neil S. Ferguson, Timothy Sharpe, Pamela J. Schartau, Satoshi Sato, Mark D. Allen, C. Mark Johnson, Trevor J. Rutherford, Alan Roy Fersht · 2005 · Journal of Molecular Biology
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    Adrian H. Elcock · 2006 · PLoS Computational Biology
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    James C. Whisstock, Arthur M. Lesk, Robin W. Carrell · 1996 · Proteins Structure Function and Bioinformatics
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74. Knotted and topologically complex proteins as models for studying folding and stability
    Todd O. Yeates, Todd S. Norcross, Neil P. King · 2007 · Current Opinion in Chemical Biology
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    Anders Irbäck, Fredrik Sjunnesson, Stefan Wallin · 2000 · Proceedings of the National Academy of Sciences
76. Is the molten globule a third phase of proteins?
    Vijay S. Pande, Daniel S. Rokhsar · 1998 · Proceedings of the National Academy of Sciences
77. Fast and Slow Folding in Cytochrome c
    S. Walter Englander, Tobin R. Sosnick, Leland C. Mayne, Mark D. Shtilerman, Phoebe Xiurong Qi, Yawen Bai · 1998 · Accounts of Chemical Research
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    Jonathan P. K. Doye, David J. Wales · 1999 · Physical review. B, Condensed matter
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    William A. Eaton · 1999 · Proceedings of the National Academy of Sciences
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    Jerelle A. Joseph, Konstantin Röder, Debayan Chakraborty, Rosemary G. Mantell, David J. Wales · 2017 · Chemical Communications
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97. Main-chain Dynamics of a Partially Folded Protein:15N NMR Relaxation Measurements of Hen Egg White Lysozyme Denatured in Trifluoroethanol
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