The nature of folded states of globular proteins

Cited by (357)

Items 201–300 of 357

1. Fluctuations in molecular size, entanglement complexity, and anisometry along molecular dynamics trajectories of short α‐helices
   Gustavo A. Arteca · 1995 · Biopolymers
2. Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks
   Gregg Lois, Jerzy Bławzdziewicz, Corey S. O’Hern · 2010 · Physical Review E
3. Solvent Friction Changes the Folding Pathway of the Tryptophan Zipper TZ2
   Ranjani Narayanan, Leslie Pelakh, Stephen J. Hagen · 2009 · Journal of Molecular Biology
4. Physical basis of the disorder-order transition
   Andrea Soranno · 2020 · Archives of Biochemistry and Biophysics
5. Molecular dynamics study on folding and allostery in RfaH
   Liqin Xiong, Zhenxing Liu · 2015 · Proteins Structure Function and Bioinformatics
6. Testing Simplified Proteins Models of the hPin1 WW Domain
   Fabio Cecconi A, Carlo Guardiani, Roberto Livi · 2006 · Biophysical Journal
7. Mapping folding energy landscapes with theory and experiment
   Silvina Matysiak, Cecilia Clementi · 2007 · Archives of Biochemistry and Biophysics
8. Protein Structure and Dynamics from Single-Molecule Fluorescence Resonance Energy Transfer
   Dong Wang, Eitan Geva · 2005 · The Journal of Physical Chemistry B
9. Theoretical Perspectives on In Vitro and In Vivo Protein Folding
   Dave Thirumalai · 1994 · NATO ASI series. Series B : Physics
10. Self-organization and mismatch tolerance in protein folding: General theory and an application
    Ariel Fernández, R. Stephen Berry · 2000 · The Journal of Chemical Physics
11. Effects of confinement and crowding on folding of model proteins
    Michał Wojciechowski, Marek Cieplak · 2008 · Biosystems
12. The self-assembly mechanism of fibril-forming silk-based block copolymers
    Marieke Schor, Peter G. Bolhuis · 2011 · Physical Chemistry Chemical Physics
13. Model for the Nucleation Mechanism of Protein Folding
    Y. S. Djikaev, Eli Ruckenstein · 2007 · The Journal of Physical Chemistry B
14. Reduced Protein Models and their Application to the Protein Folding Problem
    Jeffrey Skolnick, Andrzej Koliński, Ángel R. Ortíz · 1998 · Journal of Biomolecular Structure and Dynamics
15. Anomalous Diffusion in Folding Dynamics of Minimalist Protein Landscape
    Yasuhiro Matsunaga, Chun‐Biu Li, Tamiki Komatsuzaki · 2007 · Physical Review Letters
16. The effect of sequence on the conformational stability of a model heteropolymer in explicit water
    Bryan A. Patel, Pablo G. Debenedetti, Frank H. Stillinger, Peter J. Rossky · 2008 · The Journal of Chemical Physics
17. Folding PDZ2 Domain Using the Molecular Transfer Model
    Zhenxing Liu, Govardhan Reddy, Dave Thirumalai · 2016 · The Journal of Physical Chemistry B
18. A minimalist model protein with multiple folding funnels
    C. Rebecca Locker, Rigoberto Hernandez · 2001 · Proceedings of the National Academy of Sciences
19. Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model
    Andrij Baumketner, Y. Hiwatari · 2002 · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
20. Local-structural diversity and protein folding: Application to all-β off-lattice protein models
    Patricia Wang Pan, Heather L. Gordon, Stuart M. Rothstein · 2006 · The Journal of Chemical Physics
21. Monte Carlo Approaches to the Protein Folding Problem
    Jeffrey Skolnick, Andrzej Koliński · 1999 · Advances in chemical physics
22. Coarse Grained Modeling and Approaches to Protein Folding
    Carlo Guardiani, Roberto Livi, Fabio Cecconi · 2010 · Current Bioinformatics
23. Computational methods in the study of self-entangled proteins: a critical appraisal
    Claudio Perego, Raffaello Potestio · 2019 · Journal of Physics Condensed Matter
24. Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model
    Lizhong Zhang, He Ma, Wei Qian, Haiyan Li · 2020 · Computational Biology and Chemistry
25. Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity
    Biman Jana, José N. Onuchic · 2016 · PLoS Computational Biology
26. Simulated Annealing—Optimal Histogram Methods
    David M. Ferguson, David G. Garrett · 1999 · Advances in chemical physics
27. Efficient generation of low-energy folded states of a model protein. II. Automated histogram filtering
    Stefan A. Larrass, Laurel M. Pegram, Heather L. Gordon, Stuart M. Rothstein · 2003 · The Journal of Chemical Physics
28. Application of a chaperone‐based refolding method to two‐ and three‐dimensional off‐lattice protein models
    Denise Gorse · 2002 · Biopolymers
29. Exotic transitions of random heteropolymers interacting with solid surfaces
    Lorin Gutman, Arup K. Chakraborty · 1996 · The Journal of Chemical Physics
30. Protein Transport Across Nanopores: A Statistical Mechanical Perspective From Coarse-Grained Modeling and Approaches
    Fabio Cecconi A, Marco Bacci, Mauro Chinappi · 2014 · Protein and Peptide Letters
31. Relative stability of de novo four–helix bundle proteins: Insights from coarse grained molecular simulations
    Giovanni Bellesia, Andrew I. Jewett, Joan‐Emma Shea · 2011 · Protein Science
32. Native-Based Dissipative Particle Dynamics Approach for α-Helical Folding
    Chandan Kumar Choudhury, Olga Kuksenok · 2020 · The Journal of Physical Chemistry B
33. Temperature effects on the nucleation mechanism of protein folding and on the barrierless thermal denaturation of a native protein
    Y. S. Djikaev, Eli Ruckenstein · 2008 · Physical Chemistry Chemical Physics
34. A ternary nucleation model for the nucleation pathway of protein folding
    Y. S. Djikaev, Eli Ruckenstein · 2007 · The Journal of Chemical Physics
35. Topologies to geometries in protein folding: Hierarchical and nonhierarchical scenarios
    Ariel Fernández, Andrés Colubri, R. Stephen Berry · 2001 · The Journal of Chemical Physics
36. Disparate ionic-strength dependencies of on and off rates in protein-protein association
    Huan‐Xiang Zhou · 2001 · Biopolymers
37. Hydrodynamic Effects on the Collapse Kinetics of Flexible Polyelectrolytes
    Jiaxing Yuan, Hajime Tanaka · 2024 · Physical Review Letters
38. Replica exchange simulation method using temperature and solvent viscosity
    Phuong Hoang Nguyen · 2010 · The Journal of Chemical Physics
39. Thermal denaturation of a native protein via spinodal decomposition in the framework of first-passage-time analysis
    Y. S. Djikaev, Eli Ruckenstein · 2008 · Physical Review E
40. Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice β-barrel protein
    Mary A. Griffin, Miriam Friedel, Joan‐Emma Shea · 2005 · The Journal of Chemical Physics
41. Energy landscapes and persistent minima
    Joanne M. Carr, Dorian Mazauric, Frédéric Cazals, David J. Wales · 2016 · The Journal of Chemical Physics
42. Structure and stability of chiral β-tapes: A computational coarse-grained approach
    Giovanni Bellesia, Maxim V. Fedorov, Yuri A. Kuznetsov, É. G. Timoshenko · 2005 · The Journal of Chemical Physics
43. RNA encodes physical information
    Ian Seim, Vita Zhang, Ameya P. Jalihal, Benjamin M. Stormo, Sierra J. Cole, Joanne Ekena, Hung T. Nguyen, Dave Thirumalai, Amy S. Gladfelter · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
44. Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development
    Siran Tian, Hung Van Nguyen, Ziqing Ye, Silvi Rouskin, Dave Thirumalai, Tatjana Trcek · 2025 · Nature Communications
45. Structure optimization of the two-dimensional off-lattice hydrophobic–hydrophilic model
    Jingfa Liu, Shengjun Xue, Duanbing Chen, Huantong Geng, Zhaoxia Liu · 2009 · Journal of Biological Physics
46. Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin
    Qing-Miao Nie, Akio Togashi, Takeshi N. Sasaki, Mitsunori Takano, Masaki Sasai, Tomoki P. Terada · 2014 · PLoS Computational Biology
47. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover
    Naoto Hori, Natalia A. Denesyuk, Dave Thirumalai · 2018 · The Journal of Physical Chemistry B
48. Global measure of molecular flexibility and shape fluctuations about conformational minima
    Gustavo A. Arteca · 1993 · Journal of Computational Chemistry
49. Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method
    Philippe Derreumaux · 1998 · The Journal of Chemical Physics
50. Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time
    Naoto Hori, Dave Thirumalai · 2023 · Nucleic Acids Research
51. Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences
    Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T. Nguyen, Dave Thirumalai · 2024 · Journal of Chemical Theory and Computation
52. Characterizing the First Steps of Amyloid Formation for the ccβ Peptide
    Birgit Strodel, Anthony W. P. Fitzpatrick, Michele Vendruscolo, Christopher Martin Dobson, David J. Wales · 2008 · The Journal of Physical Chemistry B
53. Entropic Mechanism of Allosteric Communication in Conformational Transitions of Dihydrofolate Reductase
    Tomoki P. Terada, Toru Kimura, Masaki Sasai · 2013 · The Journal of Physical Chemistry B
54. Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology
    Zhenxing Liu, Dave Thirumalai · 2022 · ACS Central Science
55. An off-lattice frustrated model protein with a six-stranded β-barrel structure
    Seung‐Yeon Kim · 2010 · The Journal of Chemical Physics
56. Multibasin Dynamics in Off-Lattice Minimalist Protein Landscapes
    Yasuhiro Matsunaga, Konstantin Kostov, Tamiki Komatsuzaki · 2002 · The Journal of Physical Chemistry A
57. Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models
    Ryuhei Harada, Akio Kitao · 2011 · Chemical Physics Letters
58. Influence of the Hydrodynamic Interaction on Kinetics and Thermodynamics of Minimal Protein Models
    Andrij Baumketner, Y. Hiwatari · 2002 · Journal of the Physical Society of Japan
59. Effect of hydrogen bond networks on the nucleation mechanism of protein folding
    Y. S. Djikaev, Eli Ruckenstein · 2009 · Physical Review E
60. Efficient generation of low-energy folded states of a model protein
    Heather L. Gordon, Wai Kei Kwan, Chunhang Gong, Stefan A. Larrass, Stuart M. Rothstein · 2003 · The Journal of Chemical Physics
61. Protein Dynamics: From the Native to the Unfolded State and Back Again
    Martin Karplus, Amedeo Caflisch, Andrej Šali, Eugene I. Shakhnovich · 1995 · Jerusalem Symposia on Quantum Chemistry and Biochemistry
62. Flexible Lattice Model To Study Protein Folding
    Nicole L. Nunes, Kaiqi Chen, John S. Hutchinson · 1996 · The Journal of Physical Chemistry
63. Impact of Hydrodynamic Interactions on the Kinetic Pathway of Protein Folding
    Jiaxing Yuan, Hajime Tanaka · 2024 · Physical Review Letters
64. A simple coarse-grained model for self-assembling silk-like protein fibers
    Marieke Schor, Bernd Ensing, Peter G. Bolhuis · 2009 · Faraday Discussions
65. Periodic force induced stabilization or destabilization of the denatured state of a protein
    Pulak Kumar Ghosh, Mai Suan Li, Bidhan Chandra Bag · 2011 · The Journal of Chemical Physics
66. Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines
    Andrea N. Kravats, Sam Tonddast‐Navaei, George Stan · 2016 · PLoS Computational Biology
67. A Computational Study of the Correlations between Structure and Dynamics in Free and Surface-Immobilized Single Polymer Chains
    Jianyuan Shang, Eitan Geva · 2005 · The Journal of Physical Chemistry B
68. Study of Pair Contact Formation among Hydrophobic Residues in a Model HP-36 Protein: Relationship between Contact Order Parameter and Rate of Folding and Collapse
    Goundla Srinivas, Biman Bagchi · 2003 · The Journal of Physical Chemistry B
69. Non‐Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and Non‐RRKM Kinetics
    David M. Leitner, Yasuhiro Matsunaga, Chun‐Biu Li, Tamiki Komatsuzaki, Akira Shojiguchi, Mikito Toda · 2011 · Advances in chemical physics
70. Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences
    Hiranmay Maity, Hung T. Nguyen, Naoto Hori, Dave Thirumalai · 2024 · The Journal of Physical Chemistry Letters
71. Impact of Guanidinium Hydrochloride on the Shapes of Prothymosin-α and α-Synuclein Is Dramatically Different
    Zhenxing Liu, Dave Thirumalai · 2024 · Biochemistry
72. Conformational flexibility of loops of myosin enhances the global bias in the actin–myosin interaction landscape
    Qingmiao Nie, Masaki Sasai, Tomoki P. Terada · 2014 · Physical Chemistry Chemical Physics
73. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms
    Aditya Barve, Sayed‐Rzgar Hosseini, Olivier Martin, Andreas Wagner · 2014 · BMC Systems Biology
74. Quasi-Physical Algorithm of an Off-Lattice Model for Protein Folding Problem
    Jingfa Liu, Wenqi Huang · 2007 · Journal of Computer Science and Technology
75. Modeling protein thermodynamics and fluctuations at the mesoscale
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76. Energy landscapes: topographies, interparticle forces and dynamics, and how they are related
    R. Stephen Berry · 2010 · Theoretical Chemistry Accounts
77. Mode localization in the cooperative dynamics of protein recognition
    Jeremy Copperman, Marina Guenza · 2016 · The Journal of Chemical Physics
78. Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch
    Christin Fuks, Sebastian Falkner, Nadine Schwierz, Martin Hengesbach · 2022 · Frontiers in Molecular Biosciences
79. Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters
    Andrij Baumketner, Joan‐Emma Shea, Y. Hiwatari · 2004 · The Journal of Chemical Physics
80. Reduced atomic pair-interaction design (RAPID) model for simulations of proteins
    Boris Ni, Andrij Baumketner · 2013 · The Journal of Chemical Physics
81. Conformational conversion of proteins due to mutation
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82. Phase diagram of a Gaussian random copolymer
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83. The Folding Thermodynamics and Kinetics of Crambin Using an All-Atom Monte Carlo Simulation
    Jun Shimada, Edo L. Kussell, Eugene I. Shakhnovich · 2000 · arXiv (Cornell University)
84. Minimum model for the α‐helix–β‐hairpin transition in proteins
    Hideo Imamura, Jeff Z. Y. Chen · 2007 · Proteins Structure Function and Bioinformatics
85. Spatio-temporal hierarchy in the dynamics of a minimalist protein model
    Yasuhiro Matsunaga, Akinori Baba, Chun‐Biu Li, John E. Straub, Mikito Toda, Tamiki Komatsuzaki, R. Stephen Berry · 2013 · The Journal of Chemical Physics
86. EXPLORING THE ENERGY LANDSCAPE
    David J. Wales · 2005 · International Journal of Modern Physics B
87. Structure optimization in a three‐dimensional off‐lattice protein model
    Wenqi Huang, Jingfa Liu · 2005 · Biopolymers
88. Structural Differences of Ovalbumin and S-Ovalbumin Revealed by Denaturing Conditions
    Corrado Paolinelli, Mario Barteri, Federico Boffi, Francesca Forastieri, Maria Cristina Gaudiano, Stefano Della Longa, Agostina Congiu Castellano · 1997 · Zeitschrift für Naturforschung C
89. Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain
    Zhenxing Liu, Dave Thirumalai · 2018 · The Journal of Physical Chemistry B
90. Conformational searches for the global minimum of protein models
    David M. Ferguson, Amanda Marsh and, Thomas Metzger, David G. Garrett, Keith D. Kastella · 1994 · Journal of Global Optimization
91. Local Interactions in Aqueous Ethanol Solution Revealed by the C=O Stretching Probe
    Zhiqiang Wang, Chi Chen, Ruiting Zhang, Lin Ma, Ke Lin · 2025 · Molecules
92. Folding small proteins via annealing stochastic approximation Monte Carlo
    Sooyoung Cheon, Faming Liang · 2011 · Biosystems
93. Stochastic tunneling minimization by molecular dynamics: an application to heteropolymer models
    Andrij Baumketner, Hisashi Shimizu, Masaharu Isobe, Y. Hiwatari · 2002 · Physica A Statistical Mechanics and its Applications
94. Translocation of a globular polymer through a hairy pore
    Alexander Mair, Clarion Tung, Angelo Cacciuto, Ivan Coluzza B · 2018 · Journal of Molecular Liquids
95. Mechanical unfolding of a simple model protein goes beyond the reach of one-dimensional descriptions
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96. Structure optimization by heuristic algorithm in a coarse-grained off-lattice model
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97. Simplification of complexity in protein molecular systems by grouping amino acids: a view from physics
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98. Coarse-grained molecular dynamics simulations of base-pair mismatch recognition protein MutS sliding along DNA
    Keisuke Inoue, Shoji Takada, Tsuyoshi Terakawa · 2022 · Biophysics and Physicobiology
99. A probabilistic approach to the effect of water hydrogen bonds on the kinetics of protein folding and protein denaturation
    Y. S. Djikaev, Eli Ruckenstein · 2010 · Advances in Colloid and Interface Science
100. The Effect of Nonnative Interactions on the Energy Landscapes of Frustrated Model Proteins
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