# Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent

arXiv: https://arxiv.org/abs/2606.01816 · HTML: https://mlsanity.com/paper/2606.01816/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 7 of its 30 references that are in the map.
- First posted on arXiv 1 Jun 2026.

## Builds on (most cited first, 7 of 7)

- [Accelerating scientific discovery with Co-Scientist](https://mlsanity.com/paper/2502.18864/) (2025)
- [Towards End-to-End Automation of AI Research](https://mlsanity.com/paper/2606.15497/) (2026)
- [AutoDiscovery: Open-ended Scientific Discovery via Bayesian Surprise](https://mlsanity.com/paper/2507.00310/) (2025)
- [DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening](https://mlsanity.com/paper/2310.06367/) (2023)
- [Generating Literature-Driven Scientific Theories at Scale](https://mlsanity.com/paper/2601.16282/) (2026)
- [BindCLIP: A Unified Contrastive-Generative Representation Learning Framework for Virtual Screening](https://mlsanity.com/paper/2602.15236/) (2026)
- [RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking](https://mlsanity.com/paper/2502.02371/) (2025)

## Abstract (arXiv)

Selecting where to intervene on a protein (i.e., choosing a targetable site) is often a more ambiguous and failure-prone bottleneck than selecting what binds, especially for membrane proteins where accessibility, topology, and post-translational modifications (PTMs) constrain actionable regions. We present Site4Drug, a modality-aware site-finding agent that outputs a ranked list of targetable regions with explicit constraints, evidence summaries, risk flags, and a traceable decision log. Rather than requiring users to specify the drug modality upfront, Site4Drug can recommend a binding modality (e.g., antibody/peptide-like vs small-molecule) from the same evidence used for site discovery, including topology, hydropathy, PTM propensity, disulfides, domain context, and sequence. Importantly, this evidence is applied consistently across modalities, including small-molecule pocket discovery, to avoid selecting chemically plausible but biologically occluded sites.