# scDock: streamlining drug discovery targeting cell–cell communication via scRNA-seq analysis and molecular docking

## TL;DR

scDock is a user-friendly tool that connects single-cell RNA data to drug discovery by identifying and targeting cell communication networks.

## Contribution

scDock provides an accessible end-to-end pipeline for drug discovery targeting cell-cell communication inferred from scRNA-seq data.

## Key findings

- scDock automates the identification of ligand–receptor interactions from scRNA-seq data.
- The pipeline enables structure-based virtual screening using PDB or AlphaFold-predicted protein structures.
- scDock generates comprehensive outputs for exploring signaling alterations and drug candidates.

## Abstract

Identifying drugs that target intercellular communication networks represents a promising therapeutic strategy, yet linking single-cell RNA sequencing (scRNA-seq) analysis to structure-based drug screening remains technically challenging and requires substantial bioinformatics expertise. We present scDock, an integrated and user-friendly pipeline that seamlessly connects scRNA-seq data processing, cell–cell communication inference, and molecular docking-based drug discovery. Through a single configuration file, users can execute the complete workflow, from raw scRNA-seq data to ranked drug candidates, without programming skills. scDock automates the identification of disease-relevant ligand–receptor interactions from scRNA-seq data and performs structure-based virtual screening against these communication targets using Protein Data Bank (PDB) or AlphaFold-predicted protein structures. The pipeline generates comprehensive outputs at each stage, enabling users to explore intercellular signaling alterations and discover therapeutic compounds targeting specific cell–cell communications. scDock addresses a critical gap by providing an accessible end-to-end solution for communication-targeted drug discovery from single-cell data.

scDock is freely available at https://doi.org/10.6084/m9.figshare.31370368 and https://github.com/Andrewneteye4343/scDock. It is implemented in R, Python, shell scripts, and supports Linux systems, including Ubuntu and Debian.