AI Scientist Position - Protein Structure and Function

About this role

AI@HHMI: HHMI has made a landmark $500 million commitment to support AI‑driven projects and to embed AI systems throughout every stage of the scientific process in labs across HHMI. The AI initiative will be centered at HHMI’s Janelia Research Campus. Janelia has been at the forefront of AI‑driven research in biology for more than 15 years. Its forward‑thinking structure, centralized funding, and collaborative culture make it ideally suited to take this bold leap forward.

To learn more about the initiative, visit here.

The AI Scientist, Protein Structure and Function, will focus on developing and applying AI approaches to advance the understanding and prediction of protein structure and function, including sequence–structure relationships and biomolecular interactions.

The Artificial Intelligence (AI) Scientist is an outstanding, independent researcher who develops, implements, and executes innovative AI‑driven research programs at the intersection of AI and the life sciences. AI Scientists create, lead, or participate in research projects of highly variable scale, ranging from individual work to HHMI‑wide strategic initiatives. The AI Scientist will work closely with scientists from across the broader HHMI community.

They participate in, build, or co‑mentor highly collaborative research teams consisting of other scientists, engineers, and technicians.

• A competitive compensation package with comprehensive health and welfare benefits. In addition to the base salary described below, this position may also be eligible for incentive pay.
• Generous training and travel opportunities to workshops and conferences.
• Access to state‑of‑the‑art computational infrastructure and extended capabilities provided through assistance from Janelia’s Support teams and Project teams.
• A healthy work‑life balance, with on‑site childcare, free gyms, on‑campus housing, vibrant social and dining spaces, and shuttle‑bus service to Janelia from Washington, DC metro area!
• Flexible work arrangements are available.
• Relocation assistance provided for non‑local candidates who wish to transition to the Washington, DC, metro area.

• Develop innovative generative AI and de novo protein design methods to engineer novel proteins with desired functional properties, contributing to the development of next‑generation research tools.
• Build predictive models of protein sequence‑function relationships, integrating diverse experimental datasets to accelerate the design and optimization of functional biomolecules.
• Drive independent research while collaborating across disciplines, working alongside experimentalists, engineers, and computational scientists to translate AI insights into real biological impact.
• Share your work openly through publications, code, and datasets that advance both science and the broader AI‑for‑biology community.
• Mentor team members and contribute to the strategic direction of AI@HHMI initiatives as they evolve.

• Ph.D. degree in Computer Science, Artificial Intelligence, Machine Learning, Computational Biology, Biophysics, Applied Mathematics, Physics, or related fields, or equivalent combination of education and relevant experience.
• Experience working with protein structure, function, or interaction data, including hands‑on use or development of models such as Alpha Fold, ESM, or similar protein language or structure models.
• Demonstrated application of AI methods to protein‑related problems, such as structure prediction, protein design, molecular interactions, or protein dynamics, including the ability to translate model outputs into testable biological hypotheses and new insights into protein structure and function.
• Experience developing or advancing AI models for biomolecular systems, including protein language models, generative models, or sequence‑structure learning frameworks.
• Deep expertise in machine learning, including supervised and unsupervised learning, deep learning, probabilistic modeling, and representation learning.
• 5+ years of experience in an academic, industry, or government research position is required.
• Demonstrated innovative research in the application of…