Protein Design ML Scientist – Foundation Models

Alta Resource Technologies, Inc.; Boulder (CO); On-site; USD 140,000 - 175,000; Full time

Benefits offered by this job

401(K)

Medical, dental, and vision

Parental leave

Job summary

Alta Resource Technologies is seeking a Scientist I, Computation Protein Design to drive innovation in protein design and engineering using AI and robust data practices. The role focuses on optimizing foundational AI models to accelerate our protein engineering pipeline and requires expertise in model fine-tuning, evaluation, and data engineering.

The successful candidate will collaborate with the Applied Biology team, develop technical documentation, and mentor junior engineers while

Qualifications

• Ph.D. in Computational Biology, Bioinformatics, CS with 1–3 years industry/post-doc or M.S. with 6+ years experience.
• Hands-on experience with protein foundation models such as ESM-2, ESM-3, ProteinMPNN, RFdiffusion, AlphaFold.
• Knowledge of protein design software and molecular modeling tools (Rosetta, PyMOL, Chimera).
• Demonstrated experience fine-tuning and working with large-scale machine learning models, preferably protein/biological sequence models.
• Strong proficiency in Python and modern ML frameworks (PyTorch, TensorFlow, JAX).
• Experience with model evaluation methodologies, cross-validation, metrics and statistical analysis.
• Solid understanding of protein structure, function and principles of protein engineering.

Responsibilities

• Fine-tune, adapt, and use foundational protein models for protein engineering applications.
• Develop and implement rigorous evaluation frameworks for model performance metrics.
• Conduct benchmarking studies to identify suitable foundational models for tasks.
• Design and execute computational experiments to validate model predictions.
• Leverage diverse data sources to improve internal models and develop frameworks.

Skills

Python

Protein foundation models

Model fine-tuning

PyTorch

JAX

Education

Ph.D. in Computational Biology, Bioinformatics, Computer Science (1-3 years industry/post-doc) or MS with 6+ years

Tools

Rosetta

PyMOL

Chimera

Job description

Alta Resource Technologies is seeking a Scientist I, Computation Protein Design to drive innovation in protein design and engineering using AI and robust data practices. The role focuses on optimizing foundational AI models to accelerate our protein engineering pipeline and requires expertise in model fine-tuning, evaluation, and data engineering.

The successful candidate will collaborate with the Applied Biology team, develop technical documentation, and mentor junior engineers while