Imagen de Portada

Dummy Atom Based Thermodynamic Integration Accurately Predicts Disulfide Redox Free Energies in Proteins

Fuente: arXiv

Guardado en:

Detalles Bibliográficos
Autores principales:	Mejia-Rodriguez, Daniel, Samantray, Suman, Cheung, Margaret S., Kim, Hoshin
Formato:	Preprint
Publicado:	2025
Materias:	Biological Physics Computational Physics
Acceso en línea:	Acceder al recurso
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

Ejemplares similares

PTM-Psi on the Cloud
por: Samantray, Suman, et al.
Publicado: (2025)

Thiol post-translational modifications modulate allosteric regulation of the OpcA-G6PDH complex through conformational gate control
por: Kim, Hoshin, et al.
Publicado: (2025)

AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics
por: Mirarchi, Antonio, et al.
Publicado: (2024)

Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields
por: Cavender, Chapin E., et al.
Publicado: (2023)

Breaking the Timescale Barrier: Generative Discovery of Conformational Free-Energy Landscapes and Transition Pathways
por: Tang, Chenyu, et al.
Publicado: (2025)

Orientation-Dependent Protein Binding at Nanoparticle Interfaces
por: Annapoorani, Vigneshwari Karunakaran, et al.
Publicado: (2026)

ProTDyn: a foundation Protein language model for Thermodynamics and Dynamics generation
por: Liu, Yikai, et al.
Publicado: (2025)

Large Language Models as AI Agents for Digital Atoms and Molecules: Catalyzing a New Era in Computational Biophysics
por: Xia, Yijie, et al.
Publicado: (2025)

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)

Link Node: A Method to Characterize the Chain Topology of Intrinsically Disordered Proteins
por: Lang, Danqi, et al.
Publicado: (2024)

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

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

Real-Time, Label-free Electrical Transduction of Catalytic Events in a Single-Protein Redox Enzymatic Junction
por: Ha, Tracy Quynh, et al.
Publicado: (2025)

The Protein Force Field Plays a Crucial Role in Obtaining Accurate Macromolecular Ensembles of IDPs
por: Adhikari, Rohan S., et al.
Publicado: (2025)

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

Volume-Scaled Common Nearest Neighbor Clustering Algorithm with Free-Energy Hierarchy
por: Weiß, R. Gregor, et al.
Publicado: (2020)

WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space
por: Mitra, Sudipta, et al.
Publicado: (2025)

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

Predicting Resistive Pulse Signatures in Nanopores by Accurately Modeling Access Regions
por: Charron, Martin, et al.
Publicado: (2024)

Predictive Free Energy Simulations Through Hierarchical Distillation of Quantum Hamiltonians
por: Li, Chenghan, et al.
Publicado: (2025)

Machine Learning Enhanced Calculation of Quantum-Classical Binding Free Energies
por: Bensberg, Moritz, et al.
Publicado: (2025)

Time-Asymmetric Fluctuation Theorem and Efficient Free Energy Estimation
por: Zhong, Adrianne, et al.
Publicado: (2023)

Protein Design by Integrating Machine Learning with Quantum Annealing and Quantum-inspired Optimization
por: Panizza, Veronica, et al.
Publicado: (2024)

Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD
por: Neander, Lenard, et al.
Publicado: (2024)

Prediction of excitable wave dynamics using machine learning
por: Mulimani, Mahesh Kumar, et al.
Publicado: (2024)

Thermodynamics of prebiotic synthesis
por: Grayson, Michael
Publicado: (2024)

Thermodynamics for Reduced Models of Breakable Amyloid Filaments Based on Maximum Entropy Principle
por: Zhang, Xinyu, et al.
Publicado: (2024)

Accurate estimation of the normalized mutual information of multidimensional data
por: Nagel, Daniel, 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)

General Quantum Alchemical Free Energy Simulations via Hamiltonian Interpolation
por: Li, Chenghan, et al.
Publicado: (2024)

Collective Variable-Guided Engineering of the Free-Energy Surface of a Small Peptide
por: Medaparambath, Muralika, et al.
Publicado: (2026)

Machine Learning for RNA Secondary Structure Prediction: a review of current methods and challenges
por: Sacco, Giuseppe, et al.
Publicado: (2025)

Thermodynamic Optimization of Sensory Adaptation via Game-Theoretic Path Integrals
por: Kim, Gunn
Publicado: (2026)

Biological Insights from Integrative Modeling of Intrinsically Disordered Protein Systems
por: Liu, Zi Hao, et al.
Publicado: (2024)

Thermodynamic Networks: Harnessing Non-Equilibrium Steady States for Computation
por: Lipka-Bartosik, Patryk, et al.
Publicado: (2026)

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

Guiding Peptide Kinetics via Collective-Variable Tuning of Free-Energy Barriers
por: Zhilkin, Alexander, et al.
Publicado: (2026)

NPCoronaPredict: A computational pipeline for the prediction of the nanoparticle-biomolecule corona
por: Rouse, Ian, et al.
Publicado: (2024)

Illuminating Protein Dynamics: A Review of Computational Methods for Studying Photoactive Proteins
por: Czach, Sylwia, et al.
Publicado: (2025)