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Building protein tools and AI Agents
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Building protein tools and AI Agents
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MauricioCafiero/README.md

Latest additions!

MoDrAg - the MOdular DRug design AGent

We have two new flavors of the MoDrAg drug design helper agent! Both are a ground-up revision of the original from November 2025. Tools can be added very easily, hence the modular in the title!

  • Semantic MoDrAg - A drug design agwent with strong human-in-the-loop functionality. See the main page!
  • OpenAI MoDrAg - uses langraph to create a drug deisgn agent driven by OpenAI's GPT5.2 See the OpenAI agent page!
  • HuggingFace demo for the Semantic Agent
  • HuggingFace demo for the OpenAI Agent
  • Use a notebook to run Semantic MoDrAg on Colab!

Ollama chats:

A simple command-line chatbot using Ollama including RAG functionality.

  • Runs from a short page of code!
  • Read in a PDF and chat with the document
  • Create a custom model right in the chat.
  • Requires Ollama to be installed on your machine. See this page to get started!

Run large LLMs in the cloud (for free!)

  • Requires an API key from Ollama
  • Free allocations from Ollama
  • see the code!

MACE training

Simplified code for training and fine-tuning MACE machine-learned interatomic potiential models

  • Repo with code and notebook

Quantum computing intro

Find background on the quantum mechanics of quantum computing as well as introductions to quantum computing with Q#, Cirq and Qiskit!

Use the MLIP-based docking code, UMADock

  • Dock molecules is a selction of 6 proteins using the UMA MLIP for all energy evaluations.
  • Includes ligand desolvation and strain energy.
  • See the repo here!

Pinned Loading

  1. CafChem CafChem Public

    Libraries/modules for the CafChem tools for computational chemistry/drug design.

    Jupyter Notebook 1

  2. CafChemTeach CafChemTeach Public

    Notebooks and such for the Module Python, Machine Learning and AI for Chemistry

    Jupyter Notebook 1

  3. MoDrAg MoDrAg Public

    A modular drug-design AI Agent: dock ligands, predict IC50, generate novel ligands, and query APIs for info!

    Python

  4. UMADock UMADock Public

    Docking molecules in protein binding sites using Meta's UMA MLIP as the energy scoring function. Also runs with an AI Agent.

    Jupyter Notebook

  5. CafChemQuantum CafChemQuantum Public

    Quantum Computing practice / teaching code in Q#, Qiskit and Cirq

    Jupyter Notebook

  6. Gaussian16-Scripts-and-Functions Gaussian16-Scripts-and-Functions Public

    Useful bash functions and scripts for running Gaussian 16 on Linux

    Shell 4