Cover Image

Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinity

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Refahi, Mohammadsaleh, Sokhansanj, Bahrad A., Brown, James R., Rosen, Gail
Format:	Preprint
Published:	2025
Subjects:	Machine Learning Artificial Intelligence Molecular Networks
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis
by: Refahi, Mohammadsaleh, et al.
Published: (2025)

Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
by: Refahi, Mohammad Saleh, et al.
Published: (2025)

Investigating Knowledge Distillation Through Neural Networks for Protein Binding Affinity Prediction
by: Abbasi, Wajid Arshad, et al.
Published: (2026)

Pesti-Gen: Unleashing a Generative Molecule Approach for Toxicity Aware Pesticide Design
by: Kim, Taehan, et al.
Published: (2025)

Bidirectional Hierarchical Protein Multi-Modal Representation Learning
by: Liu, Xuefeng, et al.
Published: (2025)

Regressor-free Molecule Generation to Support Drug Response Prediction
by: Li, Kun, et al.
Published: (2024)

PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs
by: Zheng, Xinzhe, et al.
Published: (2025)

Towards Interpretable Drug-Drug Interaction Prediction: A Graph-Based Approach with Molecular and Network-Level Explanations
by: Chen, Mengjie, et al.
Published: (2025)

Graph Neural Network-Based Reinforcement Learning for Controlling Biological Networks - the GATTACA Framework
by: Mizera, Andrzej, et al.
Published: (2025)

CADGL: Context-Aware Deep Graph Learning for Predicting Drug-Drug Interactions
by: Wasi, Azmine Toushik, et al.
Published: (2024)

HiRes: Inspectable Precedent Memory for Reaction Condition Recommendation
by: Sathyanarayana, Shreyas Vinaya, et al.
Published: (2026)

RAG-GNN: Integrating Retrieved Knowledge with Graph Neural Networks for Precision Medicine
by: Hays, Hasi, et al.
Published: (2026)

ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering
by: Yin, Zecheng
Published: (2023)

Graph neural network explanations reveal a topological signature of disease-associated hubs in biological networks
by: Higgins, Kyle, et al.
Published: (2026)

HODDI: A Dataset of High-Order Drug-Drug Interactions for Computational Pharmacovigilance
by: Wang, Zhaoying, et al.
Published: (2025)

Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models
by: Ai, Lun, et al.
Published: (2024)

Adaptive Data-Knowledge Alignment in Genetic Perturbation Prediction
by: Xiang, Yuanfang, et al.
Published: (2025)

LLaMo: Large Language Model-based Molecular Graph Assistant
by: Park, Jinyoung, et al.
Published: (2024)

Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction
by: Wang, Liang, et al.
Published: (2024)

PLANET v2.0: A comprehensive Protein-Ligand Affinity Prediction Model Based on Mixture Density Network
by: Gao, Haotian, et al.
Published: (2026)

Information-Theoretic Requirements for Gradient-Based Task Affinity Estimation in Multi-Task Learning
by: Zhang, Jasper, et al.
Published: (2026)

Deep Reinforcement Learning for Controlled Traversing of the Attractor Landscape of Boolean Models in the Context of Cellular Reprogramming
by: Mizera, Andrzej, et al.
Published: (2024)

The Signed Two-Space Proximity Model for Learning Representations in Protein-Protein Interaction Networks
by: Nakis, Nikolaos, et al.
Published: (2025)

Active learning of digenic functions with boolean matrix logic programming
by: Ai, Lun, et al.
Published: (2024)

PACER: Acyclic Causal Discovery from Large-Scale Interventional Data
by: Torné, Ramon Viñas, et al.
Published: (2026)

Unveiling Molecular Moieties through Hierarchical Grad-CAM Graph Explainability
by: Contino, Salvatore, et al.
Published: (2024)

A Multimodal Human Protein Embeddings Database: DeepDrug Protein Embeddings Bank (DPEB)
by: Sajol, Md Saiful Islam, et al.
Published: (2025)

Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design
by: Xu, Ziyu, et al.
Published: (2026)

ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction
by: Jin, Mingyu, et al.
Published: (2024)

Predicting Anti-microbial Resistance using Large Language Models
by: Yoo, Hyunwoo, et al.
Published: (2024)

Graph Representation Learning Strategies for Omics Data: A Case Study on Parkinson's Disease
by: de Lope, Elisa Gómez, et al.
Published: (2024)

Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry
by: Wang, Zeyu, et al.
Published: (2024)

Benchmarking Constraint-Based Bayesian Structure Learning Algorithms: Role of Network Topology
by: Nagarajan, Radha, et al.
Published: (2025)

GenAI-Net: A Generative AI Framework for Automated Biomolecular Network Design
by: Filo, Maurice, et al.
Published: (2026)

Inference of dynamical gene regulatory networks from single-cell data with physics informed neural networks
by: Mircea, Maria, et al.
Published: (2024)

Predicting O-GlcNAcylation Sites in Mammalian Proteins with Transformers and RNNs Trained with a New Loss Function
by: Seber, Pedro
Published: (2024)

Biological Regulatory Network Inference through Circular Causal Structure Learning
by: Jiang, Hongyang, et al.
Published: (2025)

DeepRetro: Retrosynthetic Pathway Discovery using Iterative LLM Reasoning
by: Sathyanarayana, Shreyas Vinaya, et al.
Published: (2025)

AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery
by: Dai, Yifan, et al.
Published: (2025)

DualBind: A Dual-Loss Framework for Protein-Ligand Binding Affinity Prediction
by: Liu, Meng, et al.
Published: (2024)