# PharmacoMatch: Efficient 3D Pharmacophore Screening via Neural Subgraph Matching

arXiv: https://arxiv.org/abs/2409.06316 · HTML: https://mlsanity.com/paper/2409.06316/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 12 of its 46 references that are in the map.
- First posted on arXiv 10 Sep 2024.

## Builds on (most cited first, 12 of 12)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [How Attentive are Graph Attention Networks?](https://mlsanity.com/paper/2105.14491/) (2021)
- [Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs](https://mlsanity.com/paper/1704.02901/) (2017)
- [Neural Subgraph Matching](https://mlsanity.com/paper/2007.03092/) (2020)
- [DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening](https://mlsanity.com/paper/2310.06367/) (2023)
- [PharmacoNet: Accelerating Large-Scale Virtual Screening by Deep Pharmacophore Modeling](https://mlsanity.com/paper/2310.00681/) (2023)

## Built on by (most cited first, 1 of 1)

- [SubDyve: Subgraph-Driven Dynamic Propagation for Virtual Screening Enhancement Controlling False Positive](https://mlsanity.com/paper/2509.16273/) (2025)

## Abstract (arXiv)

The increasing size of screening libraries poses a significant challenge for the development of virtual screening methods for drug discovery, necessitating a re-evaluation of traditional approaches in the era of big data. Although 3D pharmacophore screening remains a prevalent technique, its application to very large datasets is limited by the computational cost associated with matching query pharmacophores to database molecules. In this study, we introduce PharmacoMatch, a novel contrastive learning approach based on neural subgraph matching. Our method reinterprets pharmacophore screening as an approximate subgraph matching problem and enables efficient querying of conformational databases by encoding query-target relationships in the embedding space. We conduct comprehensive investigations of the learned representations and evaluate PharmacoMatch as pre-screening tool in a zero-shot setting. We demonstrate significantly shorter runtimes and comparable performance metrics to existing solutions, providing a promising speed-up for screening very large datasets.