arXiv Machine Learning

Advancing Ligand-based Virtual Screening and Molecular Generation with Pretrained Molecular Embedding Distance

arXiv:2604. 24474v2 Announce Type: replace Abstract: Molecular similarity plays a central role in ligand-based drug discovery, such as virtual screening, analog searching, and goal-directed molecular generation.

arXiv Machine Learning

Jun 5

An accurate nucleic acid-small molecule docking framework via geometric deep learning with large-scale pretraining

arXiv:2606. 05198v1 Announce Type: cross Abstract: Nucleic acids are increasingly recognized as therapeutic targets beyond conventional protein-centered drug discovery, yet accurate and efficient docking of small molecules to nucleic acid structures remains challenging.

By Shi Li (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Xujun Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China), Mingquan Liu (Faculty of Health Sciences, University of Macau, Macau SAR, China), Hui Zhang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Shuoying Jia (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Yu Kang (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Shanghai Innovation Institute, Shanghai, China), Tingjun Hou (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China), Peichen Pan (College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China, Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development, Jinhua Institute of Zhejiang University, Zhejiang, China)

fine-tuning benchmarks

arXiv AI

23h ago

Domain-Adapted Molecular Language Models for Efficient Search of Make-on-Demand Libraries

arXiv:2608. 17567v1 Announce Type: cross Abstract: Pretrained molecular language models are increasingly used as molecular encoders for learning structure-property relationships.

By Henrik Wille, Luis-Finley Sch\"utz, Felix Strieth-Kalthoff

llms rag robotics fine-tuning benchmarks

arXiv Machine Learning

2d ago

READ: A Retrieval-Alignment Diffusion Framework for Structure-based Drug Design

arXiv:2506. 14488v2 Announce Type: replace-cross Abstract: Structure-based drug design (SBDD) models are central to modern pharmaceutical research, enabling the rational exploration of protein-ligand interactions at atomic resolution.

By Dong Xu, Zhangfan Yang, Junchuang Cai, Sisi Yuan, Zexuan Zhu, Jianqiang Li, Junkai Ji

diffusion benchmarks safety

arXiv Machine Learning

Jun 18

KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction

arXiv:2506. 13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery.

By Han Liu, Keyan Ding, Peilin Chen, Yinwei Wei, Liqiang Nie, Dapeng Wu, Shiqi Wang

rag benchmarks safety

arXiv AI

Aug 5

Learning Molecular Representations from Cellular Phenotypes with Structure Preservation

arXiv:2608. 02688v1 Announce Type: cross Abstract: Phenotypic drug discovery enables the discovery of functional relationships between molecular structures and cellular responses.

By Xuan Lin, Jingyu Sheng, Tengfei Ma, Li Sun, Dapeng Xiong

rag multimodal safety

arXiv Machine Learning

2d ago

Recent Advances in Deep Learning-Based Drug-Target Binding Affinity Prediction

arXiv:2608. 13797v1 Announce Type: new Abstract: Computational approaches to drug discovery involve multiple sub-problems, and among them, drug-target binding affinity prediction plays an important role.

By Jafin Khan, Md Hossain Shuvo

multimodal benchmarks safety

arXiv Machine Learning

Aug 7

Physics-Based Molecular Fingerprints from Spectral Graph Theory Provide Efficient Geometry-Aware Measures of Chemical Similarity

arXiv:2608. 05336v1 Announce Type: cross Abstract: Molecular representations are essential for the evaluation of molecular similarity and the development of structure-property relationships.

By Jacob W. Toney, Ayleen Y. Farnood, Samir Darouich, Heather J. Kulik

rag

arXiv AI

Jul 24

Beyond SBDD: Geometric Deep Learning in Polypharmacology and Multi-target Drug Design

arXiv:2607. 20550v1 Announce Type: cross Abstract: The traditional "one drug, one target" paradigm of structure-based drug design (SBDD) frequently proves inadequate for treating multifactorial diseases such as cancer and neurodegenerative disorders, owing to compensatory signaling pathways and the emergence of drug resistance.

By Tianming Han, Zhijie Pan, Wenchi Ge, Qi Zhao

rag diffusion reinforcement-learning multimodal benchmarks

arXiv AI

Jul 10

DrugGen 2: A disease-aware language model for enhancing drug discovery

arXiv:2607. 08404v1 Announce Type: cross Abstract: Current computational approaches for drug design typically focus on generating molecules conditioned on specific targets or general molecular properties, often neglecting the influence of disease context on target behavior and therapeutic outcomes.

By Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Sheikholeslami, Navid Mazrouei, Matin Irajpour, Yousof Gheisari, Hajar Sirous

llms reinforcement-learning fine-tuning

arXiv AI

Jun 30

Beyond Drug Discovery: The Nanotechnology Molecular Optimization (NMO) Benchmark

arXiv:2606. 30170v1 Announce Type: cross Abstract: Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets.

By Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda, Julian Lorenz, Rainer Lienhart, Fabian Pauly

benchmarks safety

arXiv Machine Learning

Jun 15

Curvature-Guided Geometric Representation for Protein-Ligand Binding Affinity Prediction

arXiv:2606. 14159v1 Announce Type: new Abstract: Protein-ligand binding affinity (PLA) prediction is critical in drug discovery.

By Shuai Li, Chuan-Xian Ren, Yuhao Li, Ziqi Huang, Yue Pan, Mingzhe Tang, Hong Yan

benchmarks safety

arXiv Machine Learning

Jun 9

Hyper-Dimensional Fingerprints as Molecular Representations

arXiv:2604. 27810v2 Announce Type: replace Abstract: Computational molecular representations underpin virtual screening, property prediction, and materials discovery.

By Jonas Teufel, Luca Torresi, Andr\'e Eberhard, Pascal Friederich

rag benchmarks

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