Cover Image

Predicting the binding of small molecules to proteins through invariant representation of the molecular structure

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Beccaria, R., Lazzeri, A., Tiana, G.
Format:	Preprint
Published:	2024
Subjects:	Chemical Physics Biomolecules
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Free energy, rates, and mechanism of transmembrane dimerization in lipid bilayers from dynamically unbiased molecular dynamics simulations
by: Jackel, Emil, et al.
Published: (2024)

Simulation-based inference of single-molecule experiments
by: Dingeldein, Lars, et al.
Published: (2024)

A unified framework for coarse grained molecular dynamics of proteins with high-fidelity reconstruction
by: Zhu, Jinzhen
Published: (2024)

VTX: Real-time high-performance molecular structure and dynamics visualization software
by: Maria, Maxime, et al.
Published: (2025)

ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
by: Viswanath, Siddharth, et al.
Published: (2024)

RNA Dynamics and Interactions Revealed through Atomistic Simulations
by: Languin-Cattoën, Olivier, et al.
Published: (2025)

Physics-informed generative model for drug-like molecule conformers
by: Williams, David C., et al.
Published: (2024)

GraphXForm: Graph transformer for computer-aided molecular design
by: Pirnay, Jonathan, et al.
Published: (2024)

Genetically encoding stimulated Raman-scattering probes for cell imaging using infrared fluorescent proteins
by: Regan, David, et al.
Published: (2025)

Leap: molecular synthesisability scoring with intermediates
by: Calvi, Antonia, et al.
Published: (2024)

Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model
by: Maria, Maxime, et al.
Published: (2025)

Entropy as a Design Principle in the Photosystem II Supercomplex
by: Hall, Johanna L., et al.
Published: (2024)

Understanding active learning of molecular docking and its applications
by: Kim, Jeonghyeon, et al.
Published: (2024)

Balancing property optimization and constraint satisfaction for constrained multi-property molecular optimization
by: Xia, Xin, et al.
Published: (2024)

E(3)-equivariant models cannot learn chirality: Field-based molecular generation
by: Dumitrescu, Alexandru, et al.
Published: (2024)

Efficient and Precise Force Field Optimization for Biomolecules Using DPA-2
by: Chang, Junhan, et al.
Published: (2024)

Diffusion and Spectroscopy of H$_2$ in Myoglobin
by: Käser, Jiri, et al.
Published: (2024)

SynAsk: Unleashing the Power of Large Language Models in Organic Synthesis
by: Zhang, Chonghuan, et al.
Published: (2024)

Generating Minimum Free Energy Paths With Denoising Diffusion Probabilistic Models
by: Grigorev, Vladimir
Published: (2024)

The Quantum Compass Mechanism in Cryptochromes
by: Chengye, Zou, et al.
Published: (2025)

Mapping Still Matters: Coarse-Graining with Machine Learning Potentials
by: Görlich, Franz, et al.
Published: (2025)

Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations
by: Ansari, Narjes, et al.
Published: (2025)

New water oxidation mechanism in Photosystem II resolves major experimental controversies
by: Pushkar, Yulia
Published: (2026)

The standard coil or globule phases cannot describe the denatured state of structured proteins and intrinsically disordered proteins
by: Righini, F., 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)

A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
by: Qiao, Anjie, et al.
Published: (2025)

NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models
by: Qiao, Zhuoran, et al.
Published: (2024)

Self-Consistency Training for Density-Functional-Theory Hamiltonian Prediction
by: Zhang, He, et al.
Published: (2024)

Uncertainty Quantification for Molecular Property Predictions with Graph Neural Architecture Search
by: Jiang, Shengli, et al.
Published: (2023)

Time-dependent DFT-based study of bacteriochlorophyll a optical properties within the B800 part of Rhodoblastus acidophilus light-harvesting complex
by: Kovaleva, Evgenia A., et al.
Published: (2025)

Learning Collective Variables with Synthetic Data Augmentation through Physics-Inspired Geodesic Interpolation
by: Yang, Soojung, et al.
Published: (2024)

Clever Hans in Chemistry: Chemist Style Signals Confound Activity Prediction on Public Benchmarks
by: Blevins, Andrew D., et al.
Published: (2025)

Boosting ensemble refinement with transferable force field corrections: synergistic optimization for molecular simulations
by: Gilardoni, Ivan, et al.
Published: (2023)

EquiFlow: Equivariant Conditional Flow Matching with Optimal Transport for 3D Molecular Conformation Prediction
by: Tian, Qingwen, et al.
Published: (2024)

E3STO: Orbital Inspired SE(3)-Equivariant Molecular Representation for Electron Density Prediction
by: Mitnikov, Ilan, et al.
Published: (2024)

Distinguishing life from non-life via molecular frontier orbital energy gaps
by: Ramírez-Colón, José L., et al.
Published: (2026)

Multi-objective fluorescent molecule design with a data-physics dual-driven generative framework
by: Li, Yanheng, et al.
Published: (2026)

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)

Training-Free Guidance for Discrete Diffusion Models for Molecular Generation
by: Kerby, Thomas J., et al.
Published: (2024)

Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations
by: Silva, Tomas F. D., et al.
Published: (2024)