A unified framework for coarse grained molecular dynamics of proteins with high-fidelity reconstruction
Fuente:
arXiv
Saved in:
| Main Author: | Zhu, Jinzhen |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Genetically encoding stimulated Raman-scattering probes for cell imaging using infrared fluorescent proteins
by: Regan, David, et al.
Published: (2025)
by: Regan, David, et al.
Published: (2025)
Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model
by: Maria, Maxime, et al.
Published: (2025)
by: Maria, Maxime, et al.
Published: (2025)
Boosting ensemble refinement with transferable force field corrections: synergistic optimization for molecular simulations
by: Gilardoni, Ivan, et al.
Published: (2023)
by: Gilardoni, Ivan, et al.
Published: (2023)
Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein-mimicking Nanoparticles
by: McBride, John M., et al.
Published: (2024)
by: McBride, John M., et al.
Published: (2024)
Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations
by: Silva, Tomas F. D., et al.
Published: (2024)
by: Silva, Tomas F. D., et al.
Published: (2024)
An Allosteric Model for the Influence of $\text{H}^+$ and $\text{CO}_2$ on Oxygen-Hemoglobin Binding
by: Huang, Heming, et al.
Published: (2024)
by: Huang, Heming, et al.
Published: (2024)
Lipid-mediated hydrophobic gating in the BK potassium channel
by: Coronel, Lucia, et al.
Published: (2024)
by: Coronel, Lucia, et al.
Published: (2024)
Origin of Biological Homochirality by Crystallization of an RNA Precursor on a Magnetic Surface
by: Ozturk, S. Furkan, et al.
Published: (2023)
by: Ozturk, S. Furkan, et al.
Published: (2023)
MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data
by: Gilardoni, Ivan, et al.
Published: (2024)
by: Gilardoni, Ivan, et al.
Published: (2024)
Sparing of DNA irradiated with Ultra-High Dose-Rates under Physiological Oxygen and Salt conditions
by: Hahn, Marc Benjamin, et al.
Published: (2025)
by: Hahn, Marc Benjamin, et al.
Published: (2025)
Predicting the binding of small molecules to proteins through invariant representation of the molecular structure
by: Beccaria, R., et al.
Published: (2024)
by: Beccaria, R., et al.
Published: (2024)
VTX: Real-time high-performance molecular structure and dynamics visualization software
by: Maria, Maxime, et al.
Published: (2025)
by: Maria, Maxime, et al.
Published: (2025)
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
by: Calonaci, Nicola, et al.
Published: (2022)
by: Calonaci, Nicola, et al.
Published: (2022)
Optimizing adaptive sampling via Policy Ranking
by: Nadeem, Hassan, et al.
Published: (2024)
by: Nadeem, Hassan, et al.
Published: (2024)
Magnetic Field-dependent Isotope Effect Supports Radical Pair Mechanism in Tubulin Polymerization
by: Zadeh-Haghighi, Hadi, et al.
Published: (2025)
by: Zadeh-Haghighi, Hadi, et al.
Published: (2025)
Relaxation to statistical equilibrium in stochastic Michaelis-Menten kinetics
by: Pal, Subham, et al.
Published: (2021)
by: Pal, Subham, et al.
Published: (2021)
Applied causality to infer protein dynamics and kinetics
by: Aranganathan, Akashnathan, et al.
Published: (2025)
by: Aranganathan, Akashnathan, et al.
Published: (2025)
HEroBM: a deep equivariant graph neural network for universal backmapping from coarse-grained to all-atom representations
by: Angioletti, Daniele, et al.
Published: (2024)
by: Angioletti, Daniele, et al.
Published: (2024)
The allosteric lever: towards a principle of specific allosteric response
by: Vossel, Maximilian, et al.
Published: (2023)
by: Vossel, Maximilian, et al.
Published: (2023)
Contribution of Water to Pressure and Cold Denaturation of Proteins
by: Bianco, Valentino, et al.
Published: (2015)
by: Bianco, Valentino, et al.
Published: (2015)
Molecular Determinants of Orthosteric-allosteric Dual Inhibition of PfHT1 by Computational Assessment
by: Kong, Decheng, et al.
Published: (2025)
by: Kong, Decheng, et al.
Published: (2025)
The onset of molecule-spanning dynamics in a multi-domain protein
by: Sohmen, Benedikt, et al.
Published: (2021)
by: Sohmen, Benedikt, et al.
Published: (2021)
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
by: Viswanath, Siddharth, et al.
Published: (2024)
by: Viswanath, Siddharth, et al.
Published: (2024)
Integrating experimental data with molecular simulations to investigate RNA structural dynamics
by: Bernetti, Mattia, et al.
Published: (2022)
by: Bernetti, Mattia, et al.
Published: (2022)
Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design
by: Li, Jie, et al.
Published: (2021)
by: Li, Jie, et al.
Published: (2021)
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design
by: Jian, Yue, et al.
Published: (2024)
by: Jian, Yue, et al.
Published: (2024)
Learning data efficient coarse-grained molecular dynamics from forces and noise
by: Durumeric, Aleksander E. P., et al.
Published: (2024)
by: Durumeric, Aleksander E. P., et al.
Published: (2024)
Nonequilibrium protein complexes as molecular automata
by: Kocka, Jan, et al.
Published: (2025)
by: Kocka, Jan, et al.
Published: (2025)
SynAsk: Unleashing the Power of Large Language Models in Organic Synthesis
by: Zhang, Chonghuan, et al.
Published: (2024)
by: Zhang, Chonghuan, et al.
Published: (2024)
Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling
by: Liu, Zhuoyi, et al.
Published: (2024)
by: Liu, Zhuoyi, et al.
Published: (2024)
Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations
by: Jackel, Emil, et al.
Published: (2024)
by: Jackel, Emil, et al.
Published: (2024)
Leap: molecular synthesisability scoring with intermediates
by: Calvi, Antonia, et al.
Published: (2024)
by: Calvi, Antonia, et al.
Published: (2024)
Understanding active learning of molecular docking and its applications
by: Kim, Jeonghyeon, et al.
Published: (2024)
by: Kim, Jeonghyeon, et al.
Published: (2024)
Investigation on non-ergodicity of protein dynamics
by: Maggi, Luca
Published: (2025)
by: Maggi, Luca
Published: (2025)
GraphXForm: Graph transformer for computer-aided molecular design
by: Pirnay, Jonathan, et al.
Published: (2024)
by: Pirnay, Jonathan, et al.
Published: (2024)
Efficient and Precise Force Field Optimization for Biomolecules Using DPA-2
by: Chang, Junhan, et al.
Published: (2024)
by: Chang, Junhan, et al.
Published: (2024)
Diffusion and Spectroscopy of H$_2$ in Myoglobin
by: Käser, Jiri, et al.
Published: (2024)
by: Käser, Jiri, et al.
Published: (2024)
Entropy as a Design Principle in the Photosystem II Supercomplex
by: Hall, Johanna L., et al.
Published: (2024)
by: Hall, Johanna L., et al.
Published: (2024)
Simulation-based inference of single-molecule experiments
by: Dingeldein, Lars, et al.
Published: (2024)
by: Dingeldein, Lars, et al.
Published: (2024)
Generating Minimum Free Energy Paths With Denoising Diffusion Probabilistic Models
by: Grigorev, Vladimir
Published: (2024)
by: Grigorev, Vladimir
Published: (2024)
Similar Items
-
Genetically encoding stimulated Raman-scattering probes for cell imaging using infrared fluorescent proteins
by: Regan, David, et al.
Published: (2025) -
Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model
by: Maria, Maxime, et al.
Published: (2025) -
Boosting ensemble refinement with transferable force field corrections: synergistic optimization for molecular simulations
by: Gilardoni, Ivan, et al.
Published: (2023) -
Statistical Survey of Chemical and Geometric Patterns on Protein Surfaces as a Blueprint for Protein-mimicking Nanoparticles
by: McBride, John M., et al.
Published: (2024) -
Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations
by: Silva, Tomas F. D., et al.
Published: (2024)