Cover Image

Generative Modeling of Molecular Dynamics Trajectories

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Jing, Bowen, Stärk, Hannes, Jaakkola, Tommi, Berger, Bonnie
Format:	Preprint
Published:	2024
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms
by: Jing, Bowen, et al.
Published: (2023)

AlphaFold Meets Flow Matching for Generating Protein Ensembles
by: Jing, Bowen, et al.
Published: (2024)

AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles
by: Jing, Bowen, et al.
Published: (2025)

Dirichlet Flow Matching with Applications to DNA Sequence Design
by: Stark, Hannes, et al.
Published: (2024)

ProxelGen: Generating Proteins as 3D Densities
by: Faltings, Felix, et al.
Published: (2025)

Learning residue level protein dynamics with multiscale Gaussians
by: Bafna, Mihir, et al.
Published: (2025)

Protein FID: Improved Evaluation of Protein Structure Generative Models
by: Faltings, Felix, et al.
Published: (2025)

ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids
by: Stark, Hannes, et al.
Published: (2025)

Deep Confident Steps to New Pockets: Strategies for Docking Generalization
by: Corso, Gabriele, et al.
Published: (2024)

Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation
by: Zhou, Cai, et al.
Published: (2026)

Improving Protein Optimization with Smoothed Fitness Landscapes
by: Kirjner, Andrew, et al.
Published: (2023)

MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models
by: Kapuśniak, Kacper, et al.
Published: (2025)

Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
by: Shi, Liang, et al.
Published: (2026)

PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation
by: Luo, Yizhen, et al.
Published: (2025)

Multi-Objective Latent Space Optimization of Generative Molecular Design Models
by: Abeer, A N M Nafiz, et al.
Published: (2022)

Accelerating Protein Molecular Dynamics Simulation with DeepJump
by: Costa, Allan dos Santos, et al.
Published: (2025)

Coder as Editor: Code-driven Interpretable Molecular Optimization
by: Zhu, Wenyu, et al.
Published: (2025)

Unified Guidance for Geometry-Conditioned Molecular Generation
by: Ayadi, Sirine, et al.
Published: (2025)

SurGBSA: Learning Representations From Molecular Dynamics Simulations
by: Jones, Derek, et al.
Published: (2025)

Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Goal Directed Generation
by: Arthur-Loui, Heath, et al.
Published: (2024)

Graph Diffusion Transformers for Multi-Conditional Molecular Generation
by: Liu, Gang, et al.
Published: (2024)

Generative Molecular Design with Steerable and Granular Synthesizability Control
by: Guo, Jeff, et al.
Published: (2025)

Molecular Diffusion Models with Virtual Receptors
by: Halfon, Matan, et al.
Published: (2024)

Docking-Aware Attention: Dynamic Protein Representations through Molecular Context Integration
by: Sicherman, Amitay, et al.
Published: (2025)

Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation
by: Guo, Jeff, et al.
Published: (2024)

Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space
by: Ketata, Mohamed Amine, et al.
Published: (2024)

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming
by: Xu, Minkai, et al.
Published: (2021)

Molecular Fingerprints Are Strong Models for Peptide Function Prediction
by: Adamczyk, Jakub, et al.
Published: (2025)

It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design
by: Guo, Jeff, et al.
Published: (2024)

Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion
by: Xu, Dong, et al.
Published: (2025)

Unveiling Scaling Behaviors in Molecular Language Models: Effects of Model Size, Data, and Representation
by: Xu, Dong, et al.
Published: (2026)

IBEX: Information-Bottleneck-EXplored Coarse-to-Fine Molecular Generation under Limited Data
by: Xu, Dong, et al.
Published: (2025)

One protein is all you need
by: Bushuiev, Anton, et al.
Published: (2024)

QuickBind: A Light-Weight And Interpretable Molecular Docking Model
by: Treyde, Wojtek, et al.
Published: (2024)

Towards Efficient Molecular Property Optimization with Graph Energy Based Models
by: Miglior, Luca, et al.
Published: (2025)

Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
by: Dunn, Ian, et al.
Published: (2023)

Towards Faster and More Compact Foundation Models for Molecular Property Prediction
by: Ghunaim, Yasir, et al.
Published: (2025)

Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling
by: Yang, Yuwei, et al.
Published: (2024)

ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
by: Kyro, Gregory W., et al.
Published: (2023)

Template-Guided 3D Molecular Pose Generation via Flow Matching and Differentiable Optimization
by: Bergues, Noémie, et al.
Published: (2025)