Imagen de Portada

Illuminating Protein Dynamics: A Review of Computational Methods for Studying Photoactive Proteins

Fuente: arXiv

Guardado en:

Detalles Bibliográficos
Autores principales:	Czach, Sylwia, Rydzewski, Jakub, Nowak, Wiesław
Formato:	Preprint
Publicado:	2025
Materias:	Chemical Physics Biological Physics
Acceso en línea:	Acceder al recurso
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

Ejemplares similares

Decoding Binding Pathways of Ligands in Prolyl Oligopeptidase
por: Walczewska-Szewc, Katarzyna, et al.
Publicado: (2025)

A Note on Spectral Map
por: Gökdemir, Tuğçe, et al.
Publicado: (2024)

Selecting High-Dimensional Representations of Physical Systems by Reweighted Diffusion Maps
por: Rydzewski, Jakub
Publicado: (2024)

Spectral Map: Embedding Slow Kinetics in Collective Variables
por: Rydzewski, Jakub
Publicado: (2024)

Learning Markovian Dynamics with Spectral Maps
por: Rydzewski, Jakub, et al.
Publicado: (2023)

Quantum-Accurate Conformational Stabilities and Vibrational Dynamics in Molecules and Proteins with Machine-Learned Force Fields
por: Suárez-Dou, Sergio, et al.
Publicado: (2026)

Dynamical Decoherence and Memory Effects in Green Fluorescent Proteins by Dielectric Relaxation
por: Burgess, Adam, et al.
Publicado: (2022)

Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein-mimicking Nanoparticles
por: McBride, John M., et al.
Publicado: (2024)

Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers
por: Christie, Robson, et al.
Publicado: (2026)

Light-Matter Interactions in Photosynthetic Protein Attached to solids and Nanostructures
por: Carmeli, Itai, et al.
Publicado: (2024)

Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
por: Rydzewski, Jakub
Publicado: (2024)

Scaling Graph Neural Networks to Large Proteins
por: Airas, Justin, et al.
Publicado: (2024)

Orientation Reconstruction of Proteins using Coulomb Explosions
por: André, Tomas, et al.
Publicado: (2026)

On the Engulfment of Antifreeze Proteins by Ice
por: Thosar, Aniket U., et al.
Publicado: (2024)

Partial Orientation Retrieval of Proteins From Coulomb Explosions
por: André, Tomas, et al.
Publicado: (2024)

NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks
por: Tajs, Patryk, et al.
Publicado: (2025)

Spectral Maps for Learning Reduced Representations of Molecular Systems
por: Gökdemir, Tuğçe, et al.
Publicado: (2023)

Protein structure classification based on X-ray laser induced Coulomb explosion
por: André, Tomas, et al.
Publicado: (2024)

Excitation of Low-Frequency Modes and the Effects of Protein Dynamics on Spectral Densities of Bacteriochlorophyll Molecules
por: Maity, Sayan, et al.
Publicado: (2026)

Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model
por: Airas, Justin, et al.
Publicado: (2026)

The Effect of a Knot on the Thermal Stability of Protein MJ0366: Insights from Molecular Dynamics and Monte Carlo Simulations
por: Begun, A. M., et al.
Publicado: (2024)

Machine Learning of Slow Collective Variables and Enhanced Sampling via Spatial Techniques
por: Gökdemir, Tuğçe, et al.
Publicado: (2024)

Contribution of Water to Pressure and Cold Denaturation of Proteins
por: Bianco, Valentino, et al.
Publicado: (2015)

Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins
por: Bin, Maddalena, et al.
Publicado: (2023)

Constructing Generalized Sample Transition Probabilities with Biased Simulations
por: Wang, Yanbin, et al.
Publicado: (2025)

Dynamic Response of Ionic Current in Conical Nanopores
por: Liu, Zhe, et al.
Publicado: (2024)

Tripeptide-Dynamics from Empirical and Machine-Learned Energy Functions
por: Aydin, Sena, et al.
Publicado: (2025)

Understanding the Salt Effects on the Liquid-Liquid Phase Separation of Proteins
por: Duan, Chao, et al.
Publicado: (2023)

Conformational Dynamics of 8-Oxoguanine Mispairing Reveal a Mechanism of Polymerase λ Misincorporation
por: Ferguson, George, et al.
Publicado: (2025)

Distinct Structural Dynamics of the Semiquinone State Define a Signalling Pathway in Avian Cryptochrome
por: Kish, Monika, et al.
Publicado: (2026)

A Hybrid Quantum Computing Pipeline for Real World Drug Discovery
por: Li, Weitang, et al.
Publicado: (2024)

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning
por: Ivonina, Mariia, et al.
Publicado: (2026)

Accurate QM/MM Molecular Dynamics for Periodic Systems in \textsc{GPU4PySCF} with Applications to Enzyme Catalysis
por: Li, Chenghan, et al.
Publicado: (2024)

Prospects for NMR Spectral Prediction on Fault-Tolerant Quantum Computers
por: Elenewski, Justin E., et al.
Publicado: (2024)

Delving into the Catalytic Mechanism of Molybdenum Cofactors: A Novel Coupled Cluster Study
por: Gałyńska, Marta, et al.
Publicado: (2024)

Computational Modeling of Exciton-bath Hamiltonians for LH2 and LH3 Complexes of Purple Photosynthetic Bacteria at Room Temperature
por: Montemayor, Daniel, et al.
Publicado: (2026)

Study of Quantum Confinement inside a Viral Capsid
por: Filho, Elso Drigo, et al.
Publicado: (2025)

A mesoscale model for quantitative phospholipid monolayer simulations at the air-water interface
por: Zhu, Yongzheng, et al.
Publicado: (2021)

A Fluorescent Ratiometric Potassium Sensor Based on IPG4-Silica Microparticles for Selective Detection and Fluorescence Imaging of Potassium Cations
por: Colella, Francesco, et al.
Publicado: (2024)

Auto-WHATMD : Automated Wasserstein-based High-dimensional feature extraction Analysis of Trajectories from Molecular Dynamics
por: Asano, Sosuke, et al.
Publicado: (2026)