Senior AI Engineer – Molecular Model Development

1 week ago

Alleppey, Kerala, India beBeeAIENGINEER Full time ₹ 2,50,00,000 - ₹ 3,50,00,000

We're seeking a Senior AI Engineer to develop cutting-edge machine learning models for protein–ligand structure prediction, de novo molecular generation, and multi-objective optimization. This role involves collaboration with a Ligand Design Lead to integrate chemical and biological expertise into the model pipeline.

Key Responsibilities:
  • Design deep learning architectures for pocket-conditioned molecular generation (e.g., Pocket2Mol, SE(3)-equivariant GNNs, 3D diffusion models).
  • Predict protein–ligand poses using DiffDock, EquiBind, or custom SE(3)-transformers.
  • Develop multi-objective reinforcement learning for compound optimization (potency, ADMET, novelty).
  • Fine-tune AlphaFold/OpenFold and related structure models for project-specific targets.
  • Integrate biological context from the Agentix Knowledge Graph into generative and scoring models.
  • Develop and maintain scoring functions for binding affinity, selectivity, ADMET, and synthetic accessibility.
Qualifications:
  • PhD or MSc in Computer Science, Machine Learning, Computational Chemistry, Bioinformatics, or related discipline.
  • 2+ years of hands-on experience in deep learning model development, ideally in a scientific or molecular domain.
  • Strong expertise in generative modeling (transformers, diffusion models, graph neural networks).
  • Experience with 3D geometric deep learning for molecular structures (SE(3)-equivariant architectures).
  • Proficiency in reinforcement learning (policy gradients, model-based RL, quality-diversity search).
Why this Role Matters:

This position will contribute to the development of an AI engine that combines structural chemistry input with cutting-edge molecular AI tools. Your work will power a proprietary agentic search system designed to explore the chemical universe faster and smarter than competitors.

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