:: Library Catalog

Cover Image

Saved in:

Bibliographic Details
Main Authors:	Zhu, Wenyu, Li, Chengzhu, Tian, Xiaohe, Wang, Yifan, Jia, Yinjun, Wang, Jianhui, Gao, Bowen, Zhang, Ya-Qin, Ma, Wei-Ying, Lan, Yanyan
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Biomolecules
Online Access:	https://arxiv.org/abs/2510.14455
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation
by: Zhu, Wenyu, et al.
Published: (2025)

SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction
by: Huang, Yanwen, et al.
Published: (2024)

Multi-level Interaction Modeling for Protein Mutational Effect Prediction
by: Mo, Yuanle, et al.
Published: (2024)

Pushing the boundaries of Structure-Based Drug Design through Collaboration with Large Language Models
by: Gao, Bowen, et al.
Published: (2025)

PharmAgents: Building a Virtual Pharma with Large Language Model Agents
by: Gao, Bowen, et al.
Published: (2025)

From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics
by: Gao, Bowen, et al.
Published: (2024)

Cross-Chirality Generalization by Axial Vectors for Hetero-Chiral Protein-Peptide Interaction Design
by: Yang, Ziyi, et al.
Published: (2026)

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

Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided Diffusion
by: Gao, Bowen, et al.
Published: (2024)

UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning
by: Feng, Shikun, et al.
Published: (2024)

UniGEM: A Unified Approach to Generation and Property Prediction for Molecules
by: Feng, Shikun, et al.
Published: (2024)

Fragment-Masked Diffusion for Molecular Optimization
by: Li, Kun, et al.
Published: (2024)

Contextual Molecule Representation Learning from Chemical Reaction Knowledge
by: Tang, Han, et al.
Published: (2024)

Generative Modeling of Molecular Dynamics Trajectories
by: Jing, Bowen, et al.
Published: (2024)

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

UniMAP: Universal SMILES-Graph Representation Learning
by: Feng, Shikun, et al.
Published: (2023)

Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models
by: Guo, Jeff, et al.
Published: (2024)

Interpretable QSPR Modeling using Recursive Feature Machines and Multi-scale Fingerprints
by: Shen, Jiaxuan, et al.
Published: (2024)

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model
by: Lv, Changze, et al.
Published: (2025)

Decoding Polyphenol-Protein Interactions with Deep Learning: From Molecular Mechanisms to Food Applications
by: Liu, Qiang, et al.
Published: (2025)

Joint Design of 5' Untranslated Region and Coding Sequence of mRNA
by: Liu, Yang, et al.
Published: (2024)

AMix-2: Establishing Protein as a Native Modality in Large Language Models
by: Qiu, Keyue, et al.
Published: (2026)

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

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

DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization
by: Zhou, Xiangxin, et al.
Published: (2024)

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

SeedFold: Scaling Biomolecular Structure Prediction
by: Zhou, Yi, et al.
Published: (2025)

Remodeling Peptide-MHC-TCR Triad Binding as Sequence Fusion for Immunogenicity Prediction
by: Ma, Jiahao, et al.
Published: (2025)

Probe Before You Edit: Probing-Guided Molecular Optimization for LLM Agents in Structure-Based Drug Design
by: Yang, Zaifei, et al.
Published: (2026)

RiboPO: Preference Optimization for Structure- and Stability-Aware RNA Design
by: Sun, Minghao, et al.
Published: (2025)

Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization
by: Yu, Jiajun, et al.
Published: (2025)

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

Empower Structure-Based Molecule Optimization with Gradient Guided Bayesian Flow Networks
by: Qiu, Keyue, et al.
Published: (2024)

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

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

MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text Prompts
by: Guo, Haoqiang, et al.
Published: (2024)

MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing
by: Sacco, Giuseppe, et al.
Published: (2025)

Demystifying Multimodal Biomolecular Co-design With Intrinsic Geodesic Coupling
by: Qiu, Keyue, et al.
Published: (2026)

ViraHinter: a dual-modal artificial intelligence framework for predicting virus-host interactions
by: Bai, Weiqiang, et al.
Published: (2026)

DeepFRI Demystified: Interpretability vs. Accuracy in AI Protein Function Prediction
by: Krishna, Ananya, et al.
Published: (2025)