:: Library Catalog

Cover Image

Saved in:

Bibliographic Details
Main Authors:	Tuo, Hao, Li, Yan, Hu, Xuanning, Zhao, Haishi, Liu, Xueyan, Yang, Bo
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	https://arxiv.org/abs/2507.13580
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

GenShin:geometry-enhanced structural graph embodies binding pose can better predicting compound-protein interaction affinity
by: Zhu, Pingfei, et al.
Published: (2025)

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

Fragment and Geometry Aware Tokenization of Molecules for Structure-Based Drug Design Using Language Models
by: Fu, Cong, et al.
Published: (2024)

Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs
by: Hu, Xiuyuan, et al.
Published: (2024)

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

SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision
by: Zheng, Kangjie, et al.
Published: (2024)

A Foundation Chemical Language Model for Comprehensive Fragment-Based Drug Discovery
by: Ho, Alexander, et al.
Published: (2025)

FragmentGPT: A Unified GPT Model for Fragment Growing, Linking, and Merging in Molecular Design
by: Liu, Xuefeng, et al.
Published: (2025)

Designing the Haystack: Programmable Chemical Space for Generative Molecular Discovery
by: Zhu, Yuchen, et al.
Published: (2026)

Discontinuous Epitope Fragments as Sufficient Target Templates for Efficient Binder Design
by: Deng, Zhenfeng, 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)

Two for the Price of One: Integrating Large Language Models to Learn Biophysical Interactions
by: Clark, Joseph D., et al.
Published: (2025)

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

Gradient Propagation in Retrosynthetic Space: An Efficient Framework for Synthesis Plan Generation
by: Tian, Chengyang, et al.
Published: (2024)

Latent Chemical Space Searching for Plug-in Multi-objective Molecule Generation
by: Liu, Ningfeng, et al.
Published: (2024)

KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge
by: Yang, Zaifei, et al.
Published: (2025)

Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension
by: Li, Jiahan, et al.
Published: (2024)

De novo Drug Design using Reinforcement Learning with Multiple GPT Agents
by: Hu, Xiuyuan, et al.
Published: (2023)

AbGPT: De Novo Antibody Design via Generative Language Modeling
by: Kuan, Desmond, et al.
Published: (2024)

Multimodal Large Language Models for Inverse Molecular Design with Retrosynthetic Planning
by: Liu, Gang, et al.
Published: (2024)

Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting
by: Ali, Sarwan, et al.
Published: (2024)

Efficient and Programmable Exploration of Synthesizable Chemical Space
by: Luo, Shitong, et al.
Published: (2025)

MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space
by: Qu, Yanru, et al.
Published: (2024)

The Dance of Atoms-De Novo Protein Design with Diffusion Model
by: Qin, Yujie, et al.
Published: (2025)

A Comprehensive Review of Protein Language Models
by: Wang, Lei, et al.
Published: (2025)

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

ODesign: A World Model for Biomolecular Interaction Design
by: Zhang, Odin, et al.
Published: (2025)

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

FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling
by: Zhang, Zaixi, et al.
Published: (2024)

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

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

Conditional Chemical Language Models are Versatile Tools in Drug Discovery
by: Zhu, Lu, et al.
Published: (2025)

Design of Ligand-Binding Proteins with Atomic Flow Matching
by: Liu, Junqi, et al.
Published: (2024)

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

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

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

IDP-Bert: Predicting Properties of Intrinsically Disordered Proteins (IDP) Using Large Language Models
by: Mollaei, Parisa, et al.
Published: (2024)

SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins
by: Jing, Bowen, et al.
Published: (2026)

DISPROTBENCH: Uncovering the Functional Limits of Protein Structure Prediction Models in Intrinsically Disordered Regions
by: Zeng, Xinyue, et al.
Published: (2025)

ChemEval: A Comprehensive Multi-Level Chemical Evaluation for Large Language Models
by: Huang, Yuqing, et al.
Published: (2024)