arXiv Machine Learning

Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

arXiv:2606. 14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery.

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

Aug 11

RAVEN: Frozen Random Graph Reservoirs with Physics-Informed Interaction Fingerprints for Protein-Ligand Binding Affinity Prediction

arXiv:2608. 09099v1 Announce Type: new Abstract: Quantitative estimation of protein-ligand binding affinity from three-dimensional complex structures is a fundamental task in structure-based computational chemistry and molecular modeling.

By Qingyang Zou, Jiaye Huang, Hangbo Xie, Jiayue Yin, Youyi Song, Jinfeng Liu

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 Machine Learning

1d ago

EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction

arXiv:2302. 12177v4 Announce Type: replace-cross Abstract: Predicting the binding sites of target proteins plays a fundamental role in drug discovery.

By Yang Zhang, Zhewei Wei, Ye Yuan, Chongxuan Li, Wenbing Huang

benchmarks

arXiv AI

Jul 24

SenCos-GEM: SENet-Calibrated and Law-of-Cosines-Constrained Geometry-Enhanced Molecular Representation for Property Prediction

arXiv:2607. 20551v1 Announce Type: cross Abstract: Effective molecular representation learning is crucial for accurate molecular property prediction.

By Tianming Han, Li Zhang, Qi Zhao

benchmarks

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

Jun 19

Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs

arXiv:2606. 19374v1 Announce Type: cross Abstract: Graph-based representations are widely used in protein modeling, yet many existing approaches rely primarily on sequence adjacency or geometric proximity, which only partially reflect the principles governing protein folding.

By Mohamed Mouhajir, Limei Wang, El Houcine Bergou, Hajar El Hammouti, Lamiae Azizi, Dongqi Fu

benchmarks safety

arXiv AI

Jun 2

Structure-Guided Adaptive Propagation for Protein-Protein Interaction Site Prediction

arXiv:2606. 01781v1 Announce Type: new Abstract: Accurate prediction of protein-protein interaction sites (PPIS) is essential for understanding cellular processes, disease mechanisms, and therapeutic target discovery.

By Enqiang Zhu, Yizi Liu, Yilong Luo, Yao Chen, Yu Zhang, Baoshan Ma

diffusion benchmarks

arXiv AI

Jun 3

Learning the Neighborhood: Contrast-Free Multimodal Self-Supervised Molecular Graph Pretraining

arXiv:2509. 22468v2 Announce Type: replace-cross Abstract: High-quality molecular representations are essential for property prediction and molecular design, yet large labeled datasets remain scarce.

By Boshra Ariguib, Mathias Niepert, Andrei Manolache

llms rag diffusion fine-tuning multimodal benchmarks

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 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 Machine Learning

Jul 14

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design

arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.

By Vilya Research, :, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka

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