Coarse master equations for peptide folding dynamics

Cited by (472)

Items 101–200 of 472

1. Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides
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2. Algorithm improvements for molecular dynamics simulations
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3. Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
   Shuo Gu, Daniel‐Adriano Silva, Luming Meng, Alexander Yue, Xuhui Huang · 2014 · PLoS Computational Biology
4. Machine Learning for Molecular Dynamics on Long Timescales
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5. Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
   Chodera, John D., Swope, William C., Noé, Frank, Prinz, Jan-Hendrik, Shirts, Michael R., Pande, Vijay S. · 2011 · The Journal of Chemical Physics
6. What Is the Time Scale for α-Helix Nucleation?
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7. Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach
   Zhuang, Wei, Cui, Raymond Z., Silva, Daniel-Adriano, Huang, Xuhui · 2011 · The Journal of Physical Chemistry B
8. Gaussian-Mixture Umbrella Sampling
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9. Density-based cluster algorithms for the identification of core sets
   Oliver Lemke, Bettina G. Keller · 2016 · The Journal of Chemical Physics
10. Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
    Hanlun Jiang, Fu Kit Sheong, Lizhe Zhu, Xin Gao, Julie Bernauer, Xuhui Huang · 2015 · PLoS Computational Biology
11. Hierarchical Nyström methods for constructing Markov state models for conformational dynamics
    Yao, Yuan, Cui, Raymond Z., Bowman, Gregory R., Silva, Daniel-Adriano, Sun, Jian, Huang, Xuhui · 2013 · The Journal of Chemical Physics
12. Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods
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13. Some recent techniques for free energy calculations
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14. Quantitative comparison of adaptive sampling methods for protein dynamics
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15. Kinetics of Helix Unfolding: Molecular Dynamics Simulations with Milestoning
    Krzysztof Kuczera, Gouri S. Jas, Ron Elber · 2009 · The Journal of Physical Chemistry A
16. Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
    Lukas S. Stelzl, Adam Kells, Edina Rosta, Gerhard Hummer · 2017 · Journal of Chemical Theory and Computation
17. What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models
    Suárez, Ernesto, Wiewiora, Rafal P., Wehmeyer, Chris, Noé, Frank, Chodera, John D., Zuckerman, Daniel M. · 2021 · Journal of Chemical Theory and Computation
18. Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS
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19. Perspective: Computer simulations of long time dynamics
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20. Optimized parameter selection reveals trends in Markov state models for protein folding
    Brooke E. Husic, Robert T. McGibbon, Mohammad Muneeb Sultan, Vijay S. Pande · 2016 · The Journal of Chemical Physics
21. On the advantages of exploiting memory in Markov state models for biomolecular dynamics
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22. Variational selection of features for molecular kinetics
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23. Estimating the Eigenvalue Error of Markov State Models
    Djurdjevac, Natasa, Sarich, Marco, Schütte, Christof · 2012 · Multiscale Modeling & Simulation
24. Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics
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25. Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint
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26. Unassisted Transport of N-Acetyl- l -tryptophanamide through Membrane: Experiment and Simulation of Kinetics
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27. Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias
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28. CONSTRUCTING MULTI-RESOLUTION MARKOV STATE MODELS (MSMS) TO ELUCIDATE RNA HAIRPIN FOLDING MECHANISMS
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29. Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics
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30. Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation
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31. Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models
    Lu Zhang, Fátima Pardo‐Ávila, Ilona Christy Unarta, Peter Pak‐Hang Cheung, Wang Guo, Dong Wang, Xuhui Huang · 2016 · Accounts of Chemical Research
32. Girsanov reweighting for metadynamics simulations
    Luca Donati, Bettina G. Keller · 2018 · The Journal of Chemical Physics
33. Universal and Accessible Entropy Estimation Using a Compression Algorithm
    Ram Avinery, Micha Kornreich, Roy Beck · 2019 · Physical Review Letters
34. Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides
    Shuzhe Wang, Gerhard König, H.‐J. ROTH, Marianne Fouché, Stephane Rodde, Sereina Riniker · 2021 · Journal of Medicinal Chemistry
35. Dynamics of protein folding: Probing the kinetic network of folding–unfolding transitions with experiment and theory
    Ginka S. Buchner, Ronan D. Murphy, Nicolae‐Viorel Buchete, Jan Kubelka · 2010 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
36. Network models for molecular kinetics and their initial applications to human health
    Gregory R. Bowman, Xuhui Huang, Vijay S. Pande · 2010 · Cell Research
37. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps
    Lorenzo Boninsegna, Gianpaolo Gobbo, Frank Noé, Cecilia Clementi · 2015 · Journal of Chemical Theory and Computation
38. Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations
    Fahimeh Baftizadeh, Pilar Cossio, Fabio Pietrucci, Alessandro Laio · 2012 · Current Physical Chemistry
39. Quantitative comparison of alternative methods for coarse-graining biological networks
    Bowman, Gregory R., Meng, Luming, Huang, Xuhui · 2013 · The Journal of Chemical Physics
40. Uncovering a Dynamically Formed Substrate Access Tunnel in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase
    Po-Hung Wang, Maurizio Bruschi, Luca DE GIOIA, Jochen Blumberger · 2013 · Journal of the American Chemical Society
41. Enspara : Modeling molecular ensembles with scalable data structures and parallel computing
    Justin R. Porter, Maxwell I. Zimmerman, Gregory R. Bowman · 2019 · The Journal of Chemical Physics
42. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional
    Daniel Allen Nissley, Yang Jiang, Fabio Trovato, Ian M. Sitarik, Karthik B. Narayan, Philip To, Yingzi Xia, Stephen D. Fried, Edward P. O’Brien · 2022 · Nature Communications
43. Common Features of Extraordinary Rate Theories
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44. Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling
    Frank Noé, Ralf Banisch, Cecilia Clementi · 2016 · Journal of Chemical Theory and Computation
45. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics
    Prinz, Jan-Hendrik, Chodera, John D., Pande, Vijay S., Swope, William C., Smith, Jeremy C., Noé, Frank · 2011 · The Journal of Chemical Physics
46. Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations
    Weihua Zheng, Emilio Gallicchio, Nanjie Deng, Michael Andrec, Ronald M. Levy · 2011 · The Journal of Physical Chemistry B
47. Girsanov reweighting for path ensembles and Markov state models
    Luca Donati, C. Hartmann, Bettina G. Keller · 2017 · The Journal of Chemical Physics
48. Hierarchical Folding Free Energy Landscape of HP35 Revealed by Most Probable Path Clustering
    Jain, Abhinav, Stock, Gerhard · 2014 · The Journal of Physical Chemistry B
49. Dependence of Internal Friction on Folding Mechanism
    Wenwei Zheng, David De Sancho, Travis A. Hoppe, Robert B. Best · 2015 · Journal of the American Chemical Society
50. Atomistic Kinetic Model for Population Shift and Allostery in Biomolecules
    Dong Long, Rafael Brüschweiler · 2011 · Journal of the American Chemical Society
51. MHC class II complexes sample intermediate states along the peptide exchange pathway
    Marek Wieczorek, Jana Sticht, Sebastian Stolzenberg, Sebastian Günther, Christoph Wehmeyer, Zeina El Habre, Miguel Álvaro‐Benito, Frank Noé, Christian Freund · 2016 · Nature Communications
52. Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems
    Carlo Camilloni, Fabio Pietrucci · 2018 · Advances in Physics X
53. Generalized Markov modeling of nonreversible molecular kinetics
    Bernhard Reuter, Konstantin Fackeldey, Marcus Weber · 2019 · The Journal of Chemical Physics
54. Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation
    David R. Glowacki, Emanuele Paci, Dmitrii V. Shalashilin · 2011 · Journal of Chemical Theory and Computation
55. Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics
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56. Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data
    Philipp Metzner, Frank Noé, Christof Schütte · 2009 · Physical Review E
57. Atomistic Description of the Folding of a Dimeric Protein
    Stefano Piana, Kresten Lindorff‐Larsen, David E. Shaw · 2013 · The Journal of Physical Chemistry B
58. Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding
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59. Poly-sarcosine and Poly(Ethylene-Glycol) Interactions with Proteins Investigated Using Molecular Dynamics Simulations
    Giovanni Settanni, Timo Schäfer, Christian Muhl, Matthias Barz, Friederike Schmid · 2018 · Computational and Structural Biotechnology Journal
60. Timing Is Everything: Unifying Codon Translation Rates and Nascent Proteome Behavior
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61. Helix Formation in a Pentapeptide: Experiment and Force-field Dependent Dynamics
    Wendy A. Hegefeld, Shen-En Chen, Kristine Y. DeLeon‐Pennell, Krzysztof Kuczera, Gouri S. Jas · 2010 · The Journal of Physical Chemistry A
62. Quantifying Protein–Protein Interactions in Molecular Simulations
    Alfredo Jost López, Patrick K. Quoika, Max Linke, Gerhard Hummer, Jürgen Köfinger · 2020 · The Journal of Physical Chemistry B
63. Speed limit of protein folding evidenced in secondary structure dynamics
    Milo M. Lin, Omar F. Mohammed, Gouri S. Jas, Ahmed H. Zewail · 2011 · Proceedings of the National Academy of Sciences
64. Automatic State Partitioning for Multibody Systems (APM): An Efficient Algorithm for Constructing Markov State Models To Elucidate Conformational Dynamics of Multibody Systems
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65. Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories
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66. Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution
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67. Simulations of allosteric transitions
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68. Identification and Validation of Reaction Coordinates Describing Protein Functional Motion: Hierarchical Dynamics of T4 Lysozyme
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69. Dynamic graphical models of molecular kinetics
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70. Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field
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71. Primary Peptide Folding Dynamics Observed with Ultrafast Temperature Jump
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72. Characterization of Folding Mechanisms of Trp-Cage and WW-Domain by Network Analysis of Simulations with a Hybrid-Resolution Model
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73. Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration
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74. Variational Identification of Markovian Transition States
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75. Structural cluster analysis of chemical reactions in solution
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76. Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model
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77. Preferred conformations ofN-glycan core pentasaccharide in solution and in glycoproteins
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78. On the Thermodynamics and Kinetics of Hydrophobic Interactions at Interfaces
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79. Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models
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80. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites
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81. Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps−ns Main Chain 15N−1H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1
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82. Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion
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83. Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR
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84. Identification of the protein folding transition state from molecular dynamics trajectories
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85. Markov state models of protein misfolding
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86. Folding kinetics and unfolded state dynamics of the GB1 hairpin from molecular simulation
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87. Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature
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88. Markov State Models for Rare Events in Molecular Dynamics
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89. Physical Origins of Codon Positions That Strongly Influence Cotranslational Folding: A Framework for Controlling Nascent-Protein Folding
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90. Adaptive partitioning by local density-peaks: An efficient density-based clustering algorithm for analyzing molecular dynamics trajectories
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91. The Isomeric Preference of an Atypical Dopamine Transporter Inhibitor Contributes to Its Selection of the Transporter Conformation
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92. Rapid Calculation of Molecular Kinetics Using Compressed Sensing
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93. Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation
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94. TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules
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95. Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov state models
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96. A critical appraisal of Markov state models
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97. Markov State Models of gene regulatory networks
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98. Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model
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99. Vibrational-Specific Model of Simultaneous N2−N and N2−N2 Relaxation Under Postshock Conditions
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100. Relaxation of Voronoi shells in hydrated molecular ionic liquids
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