Computational Protein Design Scientist — AI-Driven

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

Benefits offered by this job

Competitive compensation

401(k) health benefits

Paid parental leave

Job summary

Alta Resource Technologies in Boulder, CO, seeks a Scientist I, Computation Protein Design to lead protein engineering using AI models and data practices. You will fine-tune foundational models (ESM, ProteinMPNN, AlphaFold variants) and design experiments to validate predictions.

The role emphasizes interdisciplinary collaboration, rigorous evaluation, and data management under FAIR principles, with competitive pay between $140,000–$175,000 plus benefits; US citizenship required.

Qualifications

• Ph.D. in Computational Biology, Bioinformatics, Computer Science with 1-3 years of relevant industry or post-doctoral experience, or M.S. with 6+ years of relevant industry experience
• Hands-on experience with protein foundation models such as ESM-2, ESM-3, ProteinMPNN, RFdiffusion, AlphaFold, or similar architectures
• 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 or biological sequence models
• Strong proficiency in Python and modern ML frameworks (PyTorch, TensorFlow, JAX)
• Experience with model evaluation methodologies, including cross-validation, performance metrics, and statistical analysis
• Solid understanding of protein structure, function, and the principles of protein engineering
• Experience with high-performance computing environments and GPU-accelerated computing
• Strong communication skills and ability to work collaboratively in interdisciplinary teams
• US Citizenship required.

Responsibilities

• Fine-tune, adapt, and use foundational protein models for protein engineering applications
• Develop and implement rigorous evaluation frameworks to assess model performance
• Conduct benchmarking to identify suitable models for various protein tasks
• Design and execute computational experiments to validate model predictions
• Leverage diverse data sources to improve internal models and develop agentic frameworks
• Collaborate with the Applied Biology team to translate models into actionable insights
• Create technical documentation including model assumptions and validation results
• Provide mentorship and review for junior engineers and scientists
• Communicate findings, risks and recommendations to leadership and project stakeholders
• Develop data management systems that meet FAIR principles
• Develop analysis code to support experimental data analysis
• Engineer data into vectorized format for MCP integration
• Utilize experimental data to validate and improve model development

Skills

Protein models

Python

ML frameworks

Rosetta

PyMOL

Chimera

HPC

Statistics

Education

Ph.D. in Computational Biology

M.S. with 6+ years of experience

Tools

PyTorch

TensorFlow

JAX

AWS

Job description

Alta Resource Technologies in Boulder, CO, seeks a Scientist I, Computation Protein Design to lead protein engineering using AI models and data practices. You will fine-tune foundational models (ESM, ProteinMPNN, AlphaFold variants) and design experiments to validate predictions.

The role emphasizes interdisciplinary collaboration, rigorous evaluation, and data management under FAIR principles, with competitive pay between $140,000–$175,000 plus benefits; US citizenship required.