Cover Image

Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Lu, Shuqi, Ji, Xiaohong, Zhang, Bohang, Yao, Lin, Liu, Siyuan, Gao, Zhifeng, Zhang, Linfeng, Ke, Guolin
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Unified Cross-Scale 3D Generation and Understanding via Autoregressive Modeling
by: Lu, Shuqi, et al.
Published: (2025)

S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search
by: Zhou, Gengmo, et al.
Published: (2024)

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

Beyond Atoms: Evaluating Electron Density Representation for 3D Molecular Learning
by: Suriana, Patricia, et al.
Published: (2025)

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval
by: Zhou, Gengmo, et al.
Published: (2025)

GeoRecon: Graph-Level Representation Learning for 3D Molecules via Reconstruction-Based Pretraining
by: Yan, Shaoheng, et al.
Published: (2025)

Beyond Ensembles: Simulating All-Atom Protein Dynamics in a Learned Latent Space
by: Sengar, Aditya, et al.
Published: (2025)

Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains
by: Zhao, Jiale, et al.
Published: (2024)

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

Diffusion Sequence Models for Enhanced Protein Representation and Generation
by: Hallee, Logan, et al.
Published: (2025)

Sculpting Molecules in Text-3D Space: A Flexible Substructure Aware Framework for Text-Oriented Molecular Optimization
by: Zhang, Kaiwei, et al.
Published: (2024)

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

SeedProteo: Accurate De Novo All-Atom Design of Protein Binders
by: Qu, Wei, et al.
Published: (2025)

Hierarchical Structure Enhances the Convergence and Generalizability of Linear Molecular Representation
by: Wu, Juan-Ni, et al.
Published: (2024)

Beyond Efficiency: Molecular Data Pruning for Enhanced Generalization
by: Chen, Dingshuo, et al.
Published: (2024)

Platform for Representation and Integration of multimodal Molecular Embeddings
by: Zheng, Erika Yilin, et al.
Published: (2025)

AtomSurf : Surface Representation for Learning on Protein Structures
by: Mallet, Vincent, et al.
Published: (2023)

MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights
by: Hu, Jingjing, et al.
Published: (2024)

Enhancing Molecular Design through Graph-based Topological Reinforcement Learning
by: Zhang, Xiangyu
Published: (2024)

CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction
by: Han, Rong, et al.
Published: (2024)

Geometric Self-Supervised Pretraining on 3D Protein Structures using Subgraphs
by: Chatzianastasis, Michail, et al.
Published: (2024)

Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering
by: Jiao, Shujian, et al.
Published: (2024)

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

Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design
by: Zhou, Xiangxin, et al.
Published: (2024)

Molecular Communication-Based Quorum Sensing Disruption for Enhanced Immune Defense
by: Zulfiqar, Shees, et al.
Published: (2024)

Atom-level Protein Representation Learning Improves Protein Structure Prediction
by: Kim, Taewon, et al.
Published: (2026)

Latent-X: An Atom-level Frontier Model for De Novo Protein Binder Design
by: Latent Labs Team, et al.
Published: (2025)

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

ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling
by: Zheng, Kangjie, et al.
Published: (2024)

Can Molecular Evolution Mechanism Enhance Molecular Representation?
by: Li, Kun, et al.
Published: (2025)

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

Uni-Mol2: Exploring Molecular Pretraining Model at Scale
by: Ji, Xiaohong, et al.
Published: (2024)

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations
by: Jones, Derek, et al.
Published: (2023)

MODA: A Unified 3D Diffusion Framework for Multi-Task Target-Aware Molecular Generation
by: Xu, Dong, et al.
Published: (2025)

An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation
by: Zhang, Zhongyue, et al.
Published: (2025)

Full-Atom Peptide Design with Geometric Latent Diffusion
by: Kong, Xiangzhe, et al.
Published: (2024)

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

Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model
by: Qiang, Bo, et al.
Published: (2023)

Bi-TEAM: A Unified Cross-Scale Representation Learning Framework for Chemically Modified Biomolecules
by: Gu, Chunbin, et al.
Published: (2026)

CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
by: Lin, Haitao, et al.
Published: (2024)