Coarse master equations for peptide folding dynamics

Cited by (472)

Items 401–472 of 472

1. Primary Peptide Folding Dynamics Observed with Ultrafast Temperature Jump
   Omar F. Mohammed, Gouri S. Jas, Milo M. Lin, Ahmed H. Zewail · 2009 · Angewandte Chemie
2. Markov State Models in Drug Design
   Bettina G. Keller, Stevan Aleksić, Luca Donati · 2018 · Methods and principles in medicinal chemistry
3. Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Simulation Trajectories
   Song Liu, Siqin Cao, Michael Suarez, Eshani C. Goonetillek, Xuhui Huang · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
4. Role of Hsp70 chaperone in client-protein folding elucidated by Markov state modeling and NMR restraint-assisted molecular dynamics simulations
   Michael S. O’Connor, Kirill A. Konovalov, Josephine L Duvall, Jinoh Jang, Yichong Lao, Silvia Cavagnero, Xuhui Huang · 2025 · Biophysical Journal
5. Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT
   Asier Urriolabeitia, Julia Contreras‐García, David De Sancho, Xabier López · 2025 · Journal of Chemical Information and Modeling
6. Universal structure in the relaxation of photoactive proteins
   Philipp Janke, Emanuel Dorbath, Gerhard Stock, Peter M. Hamm · 2025 · The Journal of Chemical Physics
7. High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity
   Parthasarathi Sahu, S Barik, Koushik Ghosh, Hemachander Subramanian · 2024 · Journal of Molecular Evolution
8. Topological Analysis Reveals Multiple Pathways in Molecular Dynamics
   Luca Donati, Surahit Chewle, Dominik St. Pierre, Vijay Natarajan, Marcus Weber · 2025 · Journal of Chemical Theory and Computation
9. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches
   Hanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao, Julie Bernauer, Xuhui Huang · 2016 · Methods in molecular biology
10. Diffusion over barriers
    Baron Peters · 2017 · Elsevier eBooks
11. A network of conformational transitions in an unfolding process of HP-35 revealed by high-temperature MD simulation and a Markov state model
    Dandan Shao, Kaifu Gao · 2018 · Chinese Physics B
12. Changes of graph structure of transition probability matrices indicate the slowest kinetic relaxations
    Teruaki Okushima, Tomoaki Niiyama, Kensuke S. Ikeda, Yasushi Shimizu · 2018 · Physical review. E
13. Kinetic pathway analysis of an α-helix in two protonation states: Direct observation and optimal dimensionality reduction
    Gouri S. Jas, Ed W. Childs, Krzysztof Kuczera · 2019 · The Journal of Chemical Physics
14. Relations among Unidirectional Fluxes at Equilibrium, Committors, and First Passage and Transition Path Times
    Alexander M. Berezhkovskii, Attila Szabó · 2022 · The Journal of Physical Chemistry B
15. Markov State Models of Molecular Simulations to Study Protein Folding and Dynamics
    Vivek Junghare, Sourya Bhattacharya, Khalid Ansari, Saugata Hazra · 2023 · Springer eBooks
16. Continuous stochastic variables
    Baron Peters · 2017 · Elsevier eBooks
17. Polypeptide folding on a conformational‐space network: Dependence of network topology on the structural discretization procedure
    Roman Affentranger, Xavier Daura · 2010 · Journal of Computational Chemistry
18. Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy
    Nicolás O. Foglia, Mariano C. González Lebrero, Rodolfo R. Biekofsky, Dario Ariel Estrin · 2020 · Journal of Chemical Theory and Computation
19. Inherent structure versus geometric metric for state space discretization
    Hanzhong Liu, Minghai Li, Jue Fan, Shuanghong Huo · 2016 · Journal of Computational Chemistry
20. Approximating dynamic proximity with a hybrid geometry energy-based kernel for diffusion maps
    Qingzhe Tan, Mojie Duan, Minghai Li, Li Han, Shuanghong Huo · 2019 · The Journal of Chemical Physics
21. The overdamped transmission coefficient: Recovering the true mean first passage time from an inaccurate reaction coordinate
    Ryan D. Yappert, Kartik D Kamat, Baron Peters · 2019 · The Journal of Chemical Physics
22. Markov state models from hierarchical density-based assignment
    Ion Mitxelena, Xabier López, David De Sancho · 2021 · The Journal of Chemical Physics
23. Helix Formation from Hydrogen Bond Kinetics in Alanine Homopeptides
    Krzysztof Kuczera, Gouri S. Jas, Robert Szoszkiewicz · 2024 · Crystals
24. Implementation of Girsanov Reweighting in OpenMM and Deeptime
    Joana-Lysiane Schäfer, Bettina G. Keller · 2024 · The Journal of Physical Chemistry B
25. Toward Grid-Based Models for Molecular Association
    Hana Zupan, Bettina G. Keller · 2025 · Journal of Chemical Theory and Computation
26. Error Breakdown and Sensitivity Analysis of Dynamical Quantities in Markov State Models
    Yehor Tuchkov, Luke Evans, Sonya M. Hanson, Erik H. Thiede · 2025 · Journal of Chemical Theory and Computation
27. Rate laws
    Baron Peters · 2017 · Elsevier eBooks
28. Derivation of a Markov state model of the dynamics of a protein-like chain immersed in an implicit solvent
    Jeremy Schofield, Hanif Bayat · 2014 · The Journal of Chemical Physics
29. Discrete stochastic variables
    Baron Peters · 2017 · Elsevier eBooks
30. GRadient Adaptive Decomposition (GRAD) Method: Optimized Refinement Along Macrostate Borders in Markov State Models
    Pablo Romano, Marina Guenza · 2017 · Journal of Chemical Information and Modeling
31. Integrative Generalized Master Equation: A Theory to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels
    Siqin Cao, Yunrui Qiu, Michael L. Kalin, Xuhui Huang · 2022 · ChemRxiv
32. Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates
    Emanuele Zippo, Dorothee Dormann, Thomas Speck, Lukas S. Stelzl · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
33. Bidirectional control of a metabolic transition by the GID ubiquitin ligase
    Ka-Yiu Edwin Kong, Christian Ochs, Cécile Debarnot, Matti Myllykoski, Denís Arribas Blanco, Susmitha Shankar, Vivien A. C. Schoonenberg, Julia Kończak, Julia K. Varga, Ora Schueler‐Furman et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
34. Understanding the Fast-Triggering Unfolding Dynamics of FK-11 upon Photoexcitation of Azobenzene
    Tiantian Xu, Yongfang Li, Xin Gao, Lu Zhang · 2024 · The Journal of Physical Chemistry Letters
35. Discrete state model of a self-aggregating colloidal system with directional interactions
    Salman Fariz Navas, Sabine H. L. Klapp · 2024 · The Journal of Chemical Physics
36. Helix Folding in One Dimension: Effects of Proline Co-Solvent on Free Energy Landscape of Hydrogen Bond Dynamics in Alanine Peptides
    Krzysztof Kuczera · 2025 · Life
37. A Practical Guide to Transition State Analysis in Biomolecular Simulations with TS-DAR
    Eshani C. Goonetilleke, Bojun Liu, Yue Wu, Michael S. O’Connor, Xuhui Huang · 2025 · The Journal of Physical Chemistry B
38. Microsecond Dynamics of the Pyrophosphate Ion Release in SARS-CoV-2 RNA Polymerase
    Tiantian Xu, Lin Yang, Xinzhou Xu, Bu-Yu Zhang, Xin Gao, Toyotaka Ishibashi, Peng Gong, Peter Pak‐Hang Cheung, Lu Zhang · 2026 · JACS Au
39. Modulation of a Ligand’s Energy Landscape and Kinetics by the Chemical Environment
    Martin Held, Petra Imhof, Bettina G. Keller, Frank Noé · 2012 · The Journal of Physical Chemistry B
40. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states
    Qin Qiao, Hou-Dao Zhang, Xuhui Huang · 2016 · The Journal of Chemical Physics
41. Peptide Folding in Cellular Environments: A Monte Carlo and Markov Modeling Approach
    Daniel Nilsson, Sandipan Mohanty, Anders Irbäck · 2018 · Springer series on bio- and neurosystems
42. Preface
    1987 · Annual Review of Physical Chemistry
43. Preface
    2011 · Annual Review of Physical Chemistry
44. Simulating the Peptide Folding Kinetic Related Spectra Based on the Markov State Model
    Jian Hua Song, Wei Zhuang · 2013 · Advances in experimental medicine and biology
45. On the Development of Coarse-Grained Protein Models
    Dave Thirumalai, Nicolae‐Viorel Buchete, John E. Straub · 2008 · CRC Press eBooks
46. Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation
    Xian Chen, Tianmin Wu, Zhe‐Ning Chen, Tan Jin, Wei Zhuang, Yisong Zheng · 2017 · Science China Chemistry
47. Sonifying Stochastic Walks on Biomolecular Energy Landscapes
    Robert E. Arbon, Alex J. Jones, Lars Andersen Bratholm, Tom Mitchell, David R. Glowacki · 2018 · International Conference on Auditory Display (ICAD)
48. Mean first passage times reconstruct the slowest relaxations in potential energy landscapes of nanoclusters
    Teruaki Okushima, Tomoaki Niiyama, Kensuke Ikeda, Yasushi Shimizu · 2019 · Physical review. E
49. Preface
    Mark A. Johnson, Todd J. Martı́nez · 2012 · Annual Review of Physical Chemistry
50. Insights On Protein Structure And Dynamics From Multiple Biased Molecular Dynamics Simulations
    Fabrizio Marinelli, Stefano Piana, Fabio Pietrucci, Nevena Torodova, Irene Yarovsky, Alessandro Laio · 2009 · Biophysical Journal
51. Correction: Discrete Kinetic Models from Funneled Energy Landscape Simulations
    Nicholas P. Schafer, Ryan M. B. Hoffman, Anat Burger, Patricio O. Craig, Elizabeth A. Komives, Peter Guy Wolynes · 2013 · PLoS ONE
52. A coarse graining method for the dimension reduction of the state space of biomolecules
    Konstantin Fackeldey, Martina Klimm, Marcus Weber · 2012 · Journal of Mathematical Chemistry
53. Molecular Modeling in Peptide and Protein Analysis
    Krzysztof Kuczera · 2011 · Wiley eBooks
54. First passage times and relaxation times of unfolded proteins and the funnel model of protein folding
    Wei Dai · 2016
55. The Effect of Codon Translation Rates on Cotranslational Protein Folding Mechanisms of Arbitrary Complexity
    Edward P. O’Brien · 2014 · Biophysical Journal
56. EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space
    Zhenyu Wang, Xin Zhou, Guanghong Zuo · 2020 · Frontiers in Molecular Biosciences
57. The influence of N-methylation on the ansamers of an amatoxin: Gly5Sar-amanullin
    Marius T. Wenz, Simone Kosol, Guiyang Yao, Roderich D. Süßmuth, Bettina G. Keller · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
58. GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction
    Krzysztof Kuczera, Robert Szoszkiewicz, Christopher L. Shaffer, Gouri S. Jas · 2023 · Journal of Biomolecular Structure and Dynamics
59. Information thermodynamics of transition paths between multiple mesostates
    Miranda Louwerse, David A. Sivak · 2024 · Physical review. E
60. Upper-Order TICA and Fractional Non-Markovian Process to Model Anomalous Dynamic Regimes
    Arnaldo Rapallo · 2025 · Journal of Chemical Theory and Computation
61. Lost in Projection? Gaussian Filtering Recovers Hidden Conformational States
    Sofia Sartore, Daniel Nagel, Georg Diez, Gerhard Stock · 2026 · The Journal of Physical Chemistry Letters
62. Numerical characterization of point defect kinetics and sink strengths in crystalline solids using absorbing Markov chains
    Savneet Kaur · 2022 · theses.fr (ABES)
63. A Machine-Learned Symbolic Committor for a Chemical Reaction: Isomerization in Retinal and p -Coumaric Acid
    Kai Töpfer, Gianmarco Lazzeri, Vittoria Ossanna, Christopher J.I. Bläß, Florian Renner, Gianluca Lattanzi, Roberto Covino, Bettina G. Keller · 2026 · Journal of Chemical Theory and Computation
64. Metastable Protein–Protein Interactions as a Design Principle for PROTACs: Insights from the RIPK1–VHL System
    Yue Wu, Z ZHANG, Nina J. Hawkins, Weiping Tang, Xuhui Huang · 2026 · JACS Au
65. Data-Driven Modeling of Biomolecular Dynamics under Physical and Experimental Constraints
    Christopher Kara · 2026
66. A continuous-space analytical framework for committor functions from molecular dynamics
    Siqin Cao, Xuhui Huang · 2026 · The Journal of Chemical Physics
67. Shake it off: Abl kinase regulatory domain dynamics explain conformational 1 changes upon activation 2
    Philipe Oliveira Fernandes, Jose Luis Muñoz Reyes, Pedro Tenório T. F. Leite, Diego Magno Martins, Antti Poso, Ina Pöhner, Adolfo Henrique Moraes, Vinícius Gonçalves Maltarollo, Thales Kronenberger · 2026 · ChemRxiv
68. π -Girsanov: A generalized method to construct Markov state models from non-equilibrium and multiensemble biased simulations
    Mingyuan Zhang, Yong Wang, Bettina G. Keller, Hao Wu · 2026 · The Journal of Chemical Physics
69. Progressive Loosening of a Dual Autoinhibitory Interface Activates PP2A-B56δ
    Michael S. O’Connor, Cheng-Guo Wu, Yichong Lao, Yongna Xing, Xuhui Huang · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
70. Deep learning of position-dependent diffusivity from umbrella sampling molecular dynamics simulations
    Jonathan J. Harris, Benoı̂t Roux · 2026 · The Journal of Chemical Physics
71. Structure and function of the DFCP1 membrane barrier responsible for ER microdomain organization in lysosome repair
    Zhicheng Cui, Karen Palacio‐Rodríguez, Eric Herrmann, Athanasios Kourniotis, Maja Radulovic, Sascha Pust, Karla Tapia, Camilla Raiborg, Gerhard Hummer, Harald Stenmark et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
72. Kinase–phosphatase cycles drive self-sustained oscillations of protein condensates
    Emanuele Zippo, Le Qiao, Dorothee Dormann, Thomas Speck, Friederike Schmid, Lukas S. Stelzl · 2026 · bioRxiv (Cold Spring Harbor Laboratory)