ai engineer iii computational drug discovery ai model development at sam quest solutions inc remote

We're looking for an **AI Engineer III** to support the development, fine-tuning, and benchmarking of AI/ML models for computational drug discovery — building a scalable workflow that goes from protein and ligand sequence straight to 3D structure and affinity prediction with minimal manual intervention, across multiple lead optimization programs.

**What You'll Be Doing:** <br/>Fine-tune pre-trained foundation models (e.g. Boltz-2, AISB) on domain-specific project data <br/>Compile datasets from multiple LO projects, spanning experimental protein-ligand complex structures and potency/affinity data <br/>Evaluate dataset variation to challenge model applicability domains <br/>Benchmark model performance against established methods (DeepAutoQSAR, GatorAffinity, MPNN, MM-GBSA, FEP, etc.) <br/>Compare co-folder pose generation vs. docking-based methods <br/>Evaluate recall and precision using project-specific thresholds; build model ranking based on confidence and applicability domain <br/>Determine whether one fine-tuned co-folder model can serve multiple projects or whether project-specific models are needed <br/>Design an automated, end-to-end workflow optimized to generate single predictions in under a minute on GPU or CPU

**What We're Looking For:** <br/>Strong experience in machine learning, computational chemistry, cheminformatics, or related scientific data science domains <br/>Experience training and fine-tuning models on domain-specific scientific datasets <br/>Experience with 3D modeling workflows, pose generation, or docking-based comparison studies <br/>Working knowledge of benchmarking methodologies and model performance evaluation <br/>Strong Python and scripting/automation skills <br/>Ability to design reproducible, scalable model workflows with runtime efficiency in mind <br/>Strong collaboration and communication skills across scientific and technical teams

Join us if you’re passionate about harnessing the power of artificial intelligence to accelerate drug discovery! Bring your expertise in machine learning/AI-based analysis to a dynamic environment where your work directly impacts healthcare innovation on a global scale.

Pay: $70.00 - $100.00 per hour

Work Location: Remote

Location: Remote (Remote)

Remote: Yes