mlsanityData to 7 Oct 2026

Development and evaluation of a deep learning model for protein-ligand binding affinity prediction

arXiv 1712.07042 ↗First posted 19 Dec 2017stat.ML cs.LG q-bio.BMcited by 50

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Abstract (arXiv)

Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to "learn" to extract features that are relevant for the task at hand. We have developed a novel deep neural network estimating the binding affinity of ligand-receptor complexes. The complex is represented with a 3D grid, and the model utilizes a 3D convolution to produce a feature map of this representation, treating the atoms of both proteins and ligands in the same manner. Our network was tested on the CASF "scoring power" benchmark and Astex Diverse Set and outperformed classical scoring functions. The model, together with usage instructions and examples, is available as a git repository at http://gitlab.com/cheminfIBB/pafnucy

Key facts. Cited by 50 papers in the map (data through 7 Oct 2026). First posted on arXiv 19 Dec 2017.

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Citing papers per year: 2021: 4; 2022: 13; 2023: 14; 2024: 3; 2025: 11; 2026: 5.

50 papers.

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  1. 2022One Transformer Can Understand Both 2D & 3D Molecular Datacited by 77
  2. 2021Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinitycited by 60
  3. 2022DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotationscited by 54
  4. 2022Graph Neural Networks for Moleculescited by 21
  5. 2021Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networkscited by 10
  6. 2023A Universal Framework for Accurate and Efficient Geometric Deep Learning of Molecular Systemscited by 10
  7. 2022Hierarchical Graph Representation Learning for the Prediction of Drug-Target Binding Affinitycited by 7
  8. 2022SS-GNN: A Simple-Structured Graph Neural Network for Affinity Predictioncited by 7
  9. 2023Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Predictioncited by 7
  10. 2022HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Predictioncited by 6
  11. 20233D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Informationcited by 6
  12. 2022Predicting Protein-Ligand Binding Affinity via Joint Global-Local Interaction Modelingcited by 5
38 more
  1. 2023Geometric Graph Learning with Extended Atom-Types Features for Protein-Ligand Binding Affinity Predictioncited by 5
  2. 2023Machine Learning Small Molecule Properties in Drug Discoverycited by 5
  3. 2023Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Modelscited by 5
  4. 2024A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamicscited by 5
  5. 2024S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Searchcited by 5
  6. 2023A hybrid quantum-classical fusion neural network to improve protein-ligand binding affinity predictions for drug discoverycited by 4
  7. 2021APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Designcited by 3
  8. 2022From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learningcited by 2
  9. 2023Geometric Deep Learning for Structure-Based Drug Design: A Surveycited by 2
  10. 2023Deep Learning in Computational Biology: Advancements, Challenges, and Future Outlookcited by 2
  11. 2023FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretationcited by 2
  12. 2025Drug-Target Interaction/Affinity Prediction: Deep Learning Models and Advances Reviewcited by 2
  13. 2021A Novel Framework Integrating AI Model and Enzymological Experiments Promotes Identification of SARS-CoV-2 3CL Protease Inhibitors and Activity-based Probecited by 1
  14. 2022Dynamic Molecular Graph-based Implementation for Biophysical Properties Predictioncited by 1
  15. 2023HydraScreen: A Generalizable Structure-Based Deep Learning Approach to Drug Discoverycited by 1
  16. 2025Inductive-Associative Meta-learning Pipeline with Human Cognitive Patterns for Unseen Drug-Target Interaction Predictioncited by 1
  17. 2025DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representationcited by 1
  18. 2025DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Predictioncited by 1
  19. 2025Generative molecule evolution using 3D pharmacophore for efficient Structure-Based Drug Designcited by 1
  20. 2025Generalization Beyond Benchmarks: Evaluating Learnable Protein-Ligand Scoring Functions on Unseen Targetscited by 1
  21. 2022Learning to Discover Medicinescited by 0
  22. 2022Bridging the gap between target-based and cell-based drug discovery with a graph generative multi-task modelcited by 0
  23. 2022Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Networkcited by 0
  24. 2022Recent Developments in Structure-Based Virtual Screening Approachescited by 0
  25. 2023HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representationscited by 0
  26. 2023ALMERIA: Boosting pairwise molecular contrasts with scalable methodscited by 0
  27. 2023Target-Free Compound Activity Prediction via Few-Shot Learningcited by 0
  28. 2024SPIN: SE(3)-Invariant Physics Informed Network for Binding Affinity Predictioncited by 0
  29. 2025A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discoverycited by 0
  30. 2025KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Predictioncited by 0
  31. 2025Hybrid Quantum Neural Networks for Efficient Protein-Ligand Binding Affinity Predictioncited by 0
  32. 2025A Geometric Graph-Based Deep Learning Model for Drug-Target Affinity Predictioncited by 0
  33. 2025GastroDL-Fusion: A Dual-Modal Deep Learning Framework Integrating Protein-Ligand Complexes and Gene Sequences for Gastrointestinal Disease Drug Discoverycited by 0
  34. 2026Edge-aware GAT-based protein binding site predictioncited by 0
  35. 2026Contrastive Geometric Learning Unlocks Unified Structure- and Ligand-Based Drug Designcited by 0
  36. 2026HBGSA: Hydrogen Bond Graph with Self-Attention for Drug-Target Binding Affinity Predictioncited by 0
  37. 2026Trustworthy Protein-Ligand Binding Affinity Prediction via Reliability-Aware Multi-Engine Fusioncited by 0
  38. 2026RAVEN: Frozen Random Graph Reservoirs with Physics-Informed Interaction Fingerprints for Protein-Ligand Binding Affinity Predictioncited by 0