To milliseconds and beyond: challenges in the simulation of protein folding

Cited by (410)

Items 101–200 of 410

1. Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models
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2. Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations
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3. Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2
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4. Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature
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5. Reaction coordinates and transition states in enzymatic catalysis
   Kirill Zinovjev, Iñaki Tuñón · 2017 · Wiley Interdisciplinary Reviews Computational Molecular Science
6. Progress in developing Poisson-Boltzmann equation solvers
   Chuan Li, Lin Li, Marharyta G. Petukh, Emil G Alexov · 2013 · Computational and Mathematical Biophysics
7. Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations
   Xiangda Peng, Yuebin Zhang, Yan Li, Qinglong Liu, Huiying Chu, Dinglin Zhang, Guohui Li · 2018 · Journal of Chemical Theory and Computation
8. Variational Identification of Markovian Transition States
   Linda Martini, Adam Kells, Roberto Covino, Gerhard Hummer, Nicolae‐Viorel Buchete, Edina Rosta · 2017 · Physical Review X
9. Finding the needle in the haystack: towards solving the protein-folding problem computationally
   Bian Li, Michaela Fooksa, Sten Heinze, Jens Meiler · 2017 · Critical Reviews in Biochemistry and Molecular Biology
10. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability
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11. Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model
    João M. Damas, Luís C. S. Filipe, Sara R. R. Campos, Diana Lousa, Bruno L. Victor, António M. Baptista, Cláudio M. Soares · 2013 · Journal of Chemical Theory and Computation
12. An Evaluation of the Potential of NMR Spectroscopy and Computational Modelling Methods to Inform Biopharmaceutical Formulations
    Akash Pandya, Mark J. Howard, Mire Zloh, Paul A. Dalby · 2018 · Pharmaceutics
13. The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models
    Giovanni Pinamonti, Fabian Paul, Frank Noé, Álex Rodríguez, Giovanni Bussi · 2019 · The Journal of Chemical Physics
14. TAPS: A traveling-salesman based automated path searching method for functional conformational changes of biological macromolecules
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15. Signal Transduction: From the Atomic Age to the Post-Genomic Era
    Jeremy W. Thorner, Tony Hunter, Lewis C. Cantley, Richard Sever · 2014 · Cold Spring Harbor Perspectives in Biology
16. Assessment of the utility of contact‐based restraints in accelerating the prediction of protein structure using molecular dynamics simulations
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17. Protein-Folding Analysis Using Features Obtained by Persistent Homology
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18. Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins
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19. Atomistic‐Level Portrayal of Drug–DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations
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20. Persistent Topology and Metastable State in Conformational Dynamics
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21. Heat dissipation guides activation in signaling proteins
    Jeffrey K. Weber, Diwakar Shukla, Vijay S. Pande · 2015 · Proceedings of the National Academy of Sciences
22. Biophysical characterization of dynamic structures of immunoglobulin G
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23. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods
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24. Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field
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25. Machine Learning Generation of Dynamic Protein Conformational Ensembles
    Li-E Zheng, Shrishti Barethiya, Erik B. Nordquist, Jianhan Chen · 2023 · Molecules
26. Multiscale enhanced sampling of intrinsically disordered protein conformations
    Kuo Hao Lee, Jianhan Chen · 2015 · Journal of Computational Chemistry
27. Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation
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28. Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors
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29. Machine learning in the analysis of biomolecular simulations
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30. Gaussian Accelerated Molecular Dynamics in OpenMM
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31. Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions
    Song‐Ho Chong, Sihyun Ham · 2015 · The Journal of Physical Chemistry B
32. Statistical Model Selection for Markov Models of Biomolecular Dynamics
    Robert T. McGibbon, Christian R. Schwantes, Vijay S. Pande · 2014 · The Journal of Physical Chemistry B
33. The molecular mechanism of temperature-dependent phase separation of heat shock factor 1
    Qiunan Ren, Linge Li, Lei Liu, Juan Li, Chaowei Shi, Yujie Sun, Xuebiao Yao, Zhonghuai Hou, ShengQi Xiang · 2025 · Nature Chemical Biology
34. Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria
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35. MLitB: machine learning in the browser
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36. Defining, Calculating, and Converging Observables of a Kinetic Transition Network
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37. The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
    Thomas E. Cheatham, Daniel R. Roe · 2015 · Computing in Science & Engineering
38. Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations
    Mohammad Muneeb Sultan, Gert Kiss, Diwakar Shukla, Vijay S. Pande · 2014 · Journal of Chemical Theory and Computation
39. Reaction Coordinate-Free Approach to Recovering Kinetics from Potential-Scaled Simulations: Application of Kramers’ Rate Theory
    Aaron T. Frank, Ioan Andricioaei · 2016 · The Journal of Physical Chemistry B
40. Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT
    Yutaka Maruyama, Ayori Mitsutake · 2017 · The Journal of Physical Chemistry B
41. Multiscale molecular dynamics simulations of rotary motor proteins
    Toru Ekimoto, Mitsunori Ikeguchi · 2017 · Biophysical Reviews
42. Advances in turbulent mixing techniques to study microsecond protein folding reactions
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43. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment
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44. Transition path theory from biased simulations
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45. Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives
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46. Conformational Reorganization Coupled to the Ionization of Internal Lys Residues in Proteins
    Daniel E. Richman, Ananya K. Majumdar, Bertrand García‐Moreno E. · 2015 · Biochemistry
47. Relaxation mode analysis for molecular dynamics simulations of proteins
    Ayori Mitsutake, Hiroshi Takano · 2018 · Biophysical Reviews
48. Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent
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49. Granger Causality Analysis of Chignolin Folding
    Marcin Sobieraj, Piotr Setny · 2022 · Journal of Chemical Theory and Computation
50. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation
    Qiang Shao, Jiye Shi, Weiliang Zhu · 2017 · Journal of Chemical Theory and Computation
51. Visualization of Large Molecular Trajectories
    David Duran, Pedro Hermosilla, Timo Ropinski, Barbora Kozlíková, Àlvar Vinacua, Pere‐Pau Vázquez · 2018 · IEEE Transactions on Visualization and Computer Graphics
52. On inference of causality for discrete state models in a multiscale context
    Susanne Gerber, Illia Horenko · 2014 · Proceedings of the National Academy of Sciences
53. Protein Folding Thermodynamics: A New Computational Approach
    Song‐Ho Chong, Sihyun Ham · 2014 · The Journal of Physical Chemistry B
54. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation
    Shinji Iida, Haruki Nakamura, Junichi Higo · 2016 · Biochemical Journal
55. Peptide Bond Isomerization in High-Temperature Simulations
    Chris Neale, Régis Pomès, Angel E. Garcı́a · 2016 · Journal of Chemical Theory and Computation
56. Microsecond and nanosecond polyproline II helix formation in aqueous nanodrops measured by mass spectrometry
    Daniel N. Mortensen, Evan R. Williams · 2016 · Chemical Communications
57. Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models
    Robert T. McGibbon, Bharath Ramsundar, Mohammad Muneeb Sultan, Gert Kiss, Vijay S. Pande · 2014 · arXiv (Cornell University)
58. Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning
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59. Introduction
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60. Toward a quantitative description of microscopic pathway heterogeneity in protein folding
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61. Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin
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62. BioGNN: How Graph Neural Networks Can Solve Biological Problems
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63. The RNA Polymerase Factory and Archaeal Transcription
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64. High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant
    Polina V. Banushkina, Sergei V. Krivov · 2013 · Journal of Chemical Theory and Computation
65. Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields
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66. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
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67. Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity
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68. Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin
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69. Optimization and Validation of Efficient Models for Predicting Polythiophene Self-Assembly
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70. Molecular Dynamics Using Nonvariational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation, and Application to the Bond Capacity Model
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71. Combining molecular dynamics simulations and experimental analyses in protein misfolding
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72. Quantification of Drive-Response Relationships Between Residues During Protein Folding
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73. Closing the gap: The approach of optical and computational microscopy to uncover biomembrane organization
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74. In silico tools to study molecular targets of neglected diseases: inhibition of TcSir2rp3, an epigenetic enzyme of Trypanosoma cruzi
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78. Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics
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79. Protein remains stable at unusually high temperatures when solvated in aqueous mixtures of amino acid based ionic liquids
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80. Lessons about Protein Folding and Binding from Archetypal Folds
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81. On the Stability of Proteins Solvated in Imidazolium-Based Ionic Liquids Studied with Replica Exchange Molecular Dynamics
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82. Challenges and frontiers of computational modelling of biomolecular recognition
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83. Protein engineering and the use of molecular modeling and simulation: The case of heterodimeric Fc engineering
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84. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches
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85. Conformational investigation of the structure–activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit
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93. Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase
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96. Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions
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97. Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models
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99. Non-Native Structure Appears in Microseconds during the Folding of E. coli RNase H
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100. Designing the structure and folding pathway of modular topological bionanostructures
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