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Esenbil Information Technologies
Esenbil Information Technologies

Prodrug: AI-Driven Ligand-Protein Docking for Drug Discovery
In collaboration with Yeditepe University Medical School, powered by Google Cloud Vertex AI.

🧬 Explore the Pipeline | 📥 Get Involved

About the Project


Prodrug is an advanced drug discovery platform that systematically docks all known active pharmaceutical ingredients (APIs) against the complete AlphaFold v3 predicted human proteome.

Using a hybrid approach combining static docking estimations, molecular dynamics simulations, and AI-driven expert fusion, Prodrug aims to provide a scalable and interpretable drug-target affinity analysis.

End-to-End Prodrug Docking Workflow

Pipeline Overview

“To simulate is to understand. To dock is to predict. To combine is to decide.”

Stage 1

  • Initial docking affinity estimations using known protein structures.

  • Integrates protein data from the AlphaFold v3 Human Proteome.

  • Physical and chemical sanity check
  • AI based false positive elimination

    • Stage 2

  • In-depth molecular dynamics simulations including:

    1. Protein/Ligand Preparation

    2. System Assembly

    3. Solvation & Ionization

    4. Energy Minimization

    5. Equilibration

    6. Full Simulation

  • Configured via AI Assistant to tailor simulation parameters.

    • Stage 3

    • Outputs from dynamic analysis are integrated using a Mixture of Experts ensemble model

    Stage 4

    • Reviewed by a combined AI Assistant + Human Expert team for final binding affinity classification and druggability decision.

    Technology Stact

  • 🧠 AI: Google Gemini & OpeanAI ChatGPT

  • 🧪 Molecular Simulation: OpenMM for dynamics

  • 🧬 Structure Data: AlphaFold v3 human proteome, UniProt, STRING, Open Targets

  • ☁️ Infrastructure: Google Cloud Platform and Vertex AI (Grant-supported)

    • Collaboration

    In collaboration with:

    • Yeditepe University Medical School

    • Google Cloud for Research (Cloud Credit Grant)

    Contact

    🔹 Interested in industry collaboration?

    📧 Email us