:: Library Catalog

Cover Image

Saved in:

Bibliographic Details
Main Authors:	Liang, Jingbo, Jacobson, Bruna
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Biological Physics Biomolecules
Online Access:	https://arxiv.org/abs/2507.13950
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

JAMUN: Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensembles
by: Daigavane, Ameya, et al.
Published: (2024)

ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression
by: Shen, Yuning, et al.
Published: (2025)

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

Integrating Chemical Language and Molecular Graph in Multimodal Fused Deep Learning for Drug Property Prediction
by: Lu, Xiaohua, et al.
Published: (2023)

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

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

Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics
by: Shoghi, Nima, et al.
Published: (2026)

Data-driven Discovery of Biophysical T Cell Receptor Co-specificity Rules
by: Pyo, Andrew G. T., et al.
Published: (2024)

Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction
by: Alcaide, Eric, et al.
Published: (2024)

BInD: Bond and Interaction-generating Diffusion Model for Multi-objective Structure-based Drug Design
by: Lee, Joongwon, et al.
Published: (2024)

Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes
by: Liu, Zi Hao, et al.
Published: (2024)

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

Optimizing adaptive sampling via Policy Ranking
by: Nadeem, Hassan, et al.
Published: (2024)

EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
by: Costa, Allan dos Santos, et al.
Published: (2024)

A Solid-State Nanopore Signal Generator for Training Machine Learning Models
by: Johnson, Jaise, et al.
Published: (2025)

Insights into Protein Unfolding under pH, Temperature, and Shear using Molecular Dynamics Simulations
by: Jia, Yinhao, et al.
Published: (2024)

Joint Geometric-Chemical Distance for Protein Surfaces
by: Swami, Himanshu, et al.
Published: (2026)

EquiBoost: An Equivariant Boosting Approach to Molecular Conformation Generation
by: Yang, Yixuan, et al.
Published: (2025)

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

RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking
by: Balytskyi, Yaroslav, et al.
Published: (2025)

Hybrid quantum cycle generative adversarial network for small molecule generation
by: Anoshin, Matvei, et al.
Published: (2023)

General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design
by: Jian, Yue, et al.
Published: (2024)

GP-MoLFormer: A Foundation Model For Molecular Generation
by: Ross, Jerret, et al.
Published: (2024)

Systematic Analysis of Biomolecular Conformational Ensembles with PENSA
by: Vögele, Martin, et al.
Published: (2022)

Structure Language Models for Protein Conformation Generation
by: Lu, Jiarui, et al.
Published: (2024)

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)

Aligning Protein Conformation Ensemble Generation with Physical Feedback
by: Lu, Jiarui, et al.
Published: (2025)

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

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

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

RNA Dynamics from Experimental and Computational Approaches
by: Bussi, Giovanni, et al.
Published: (2024)

Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins
by: Dreyer, Frédéric A., et al.
Published: (2025)

Equivariant Blurring Diffusion for Hierarchical Molecular Conformer Generation
by: Park, Jiwoong, et al.
Published: (2024)

Diffusion-Driven Generative Framework for Molecular Conformation Prediction
by: Yang, Bobin, et al.
Published: (2023)

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

Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics
by: Tang, Haocheng, et al.
Published: (2026)

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
by: Wang, Yan, et al.
Published: (2024)

MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data
by: Gilardoni, Ivan, et al.
Published: (2024)

Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings
by: Sengar, Aditya, et al.
Published: (2025)

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