A Modular Drug-design AI Agent. See the descption of the Agent's abilities, the design philosphy, a description of all the files in this repo, or some sample images below.
Find a working demo of MoDrAg on HuggingFace Spaces!
Use MoDrAg's tools with OpenAI models with Modrag Chat
See the MoDrAg demo video!
A nicely featured drug-design pipeline with voice reposponse, including:
Premium Features
- Dock a molecule in a protein using AutoDock Vina, get the score and the pose.
- Use LightGBM to create a model to predict IC50 values of novel molecules. Trains itself using a Chembl Dataset which Modrag can find for you.
- Use a GPT, finetuned on a Chembl dataset (found by MoDrAg), to generate novel ligands for a protein.
*these features will take a bit longer than the standards features. The last two require a Chembl dataset ID, which you can find using modrag.
Standard Features
- Find Uniprot IDs for a protein,
- Find Chembl IDs for a given Uniprot ID,
- Find bioactive molecules for a given Chembl ID,
- Find PDB IDs for a given protein,
- Find sequences, ligand and numbers of chains for a PDB ID.
- Get SMILES strings for molecules, or
- get names for SMILES strings.
- Search Pubchem for similar molecules or generate analogues.
- Find Lipinski properties of molecules.
- Find pharmacophore overlap between two molecules.
Speech-to-text provided by a generous donation from Eleven Labs.
- Everything ‘open,' avoiding using paid services, i.e. not using the OpenAI or Anthropic APIs, etc. where possible.
- Modular sub-Agents each perform a family of tasks, easily upgradeable.
- Hardwire tool and Agent calls into the Graph – meaning that you can plug in any AI/LLM; it does not have to be trained to call tools.
- Use a small LM (~4B parameters) to save GPU/CPU for sub-agents performing calculations.
- HuggingFace’s smolLM has trouble parsing the chemistry
- Microsoft’s Phi4-mini-instruct works well!
- Looking to try IBM’s Granite 4 Nano!
MoDrAg_HFS.py: complete app for the Drug design agent. Upload to HuggingFace spaces and rename app.py.MoleculeAgent_HFS.py, PropAgent_HFS.py, ProteinAgent_HFS.py, DockAgent_HFS.py: sub-Agents for carrying out various tasks. Also ready to upload to a Hugginface space and rename as app.py.- Various
requirements.txtfiles: the requirements for each of the Agents. Agent_template.py: populate this file with one or more tools, add tool descriptions, and add the tools to the Graph and this file can be uploaded to a HuggingFace Space and serve as an Agent or MCP immediately.node_template.py: this inlcudes templates for adding your agent as a sub-agent to MoDrAg, code for adding your agent description to the Gradio GUI, and step-by-step directions on how to add all of the bits needed to integrate the new agent into the Graph.
