This project is licensed under the PolyForm Noncommercial License 1.0.0 — see LICENSE. Free for academic, research, and other noncommercial use. Commercial use requires a separate commercial license. Contact: yousefi.bme@gmail.com, sbonn@uke.de
BioChemAIgent: An AI-driven Protein Modeling and Docking Framework for Structure-Based Drug Discovery
Computational and AI-based methods have advanced drug discovery, yet most remain task-specific and require substantial expert integration. We introduce BioChemAIgent, an agentic framework that integrates state-of-the-art AI models with established computational chemistry tools to enable end-to-end small molecule analysis, protein modeling, and molecular docking, with a chatbot interface accessible online. To foster community engagement and extensibility, we established an openly accessible user interface alongside a centralized registry that consolidates resources for developing and integrating next-generation tools in drug discovery and structural biology.
- Fist clone external MCP servers
cd external-mcp-servers
git clone https://github.com/Augmented-Nature/PDB-MCP-Server.git
git clone https://github.com/Augmented-Nature/ChEMBL-MCP-Server.git
git clone https://github.com/Augmented-Nature/Augmented-Nature-UniProt-MCP-Server.git
- Make user_data folder to writable from the docker
chmod 777 user_data
chmod -R 777 external-mcp-servers/
mv Augmented-Nature-UniProt-MCP-Server/ UniProt-MCP-Server/
mv docker_compose_deploy docker_compose
- Build the docker compose and then run it. The UI is accewssible via URL: http://localhost:3000
docker compose build --no-cache api web
docker compose up -d api web
To stop the platform
docker compose stop api web
This repository provides a community-oriented registry specialized for the development of agentic systems for drug discovery and structural biology.
- Domain experts can bring forward ideas to be implemented;
- Developers can propose or refine MCP servers to broaden and improve the agent’s functionality.
- Create a new issue
- Select the template
Add featureto suggest new functionalities to be added,Add MCP serverto suggest an existing MCP server.
- Make a description of your suggestion and publish the issue.
BioChemAIgent is an open-source research framework for structure-based drug discovery. The method is described in a bioRxiv preprint and has not yet undergone peer review. The API may evolve as the framework is refined.
If you use BioChemAIgent, please cite:
Yousefi, B., Laubach, N. C., Heins, S., Testa, L., Gersting, S. W., & Bonn, S. (2025). BioChemAIgent: An AI-driven Protein Modeling and Docking Framework for Structure-Based Drug Discovery. bioRxiv, 2025-12.
This software is licensed under the PolyForm Noncommercial License 1.0.0 — see LICENSE.
Free for academic, research, and other noncommercial use. Commercial use — including use in proprietary pipelines, SaaS products, or any revenue-generating activity — requires a separate commercial license. Contact: yousefi.bme@gmail.com, sbonn@uke.de
SPDX-License-Identifier: PolyForm-Noncommercial-1.0.0