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AI Scientist – Protein Structure and Function

Howard Hughes Medical Institute (HHMI) · Ashburn, VA · 1 mo ago
On-siteResearch$182k/yrFull-time

About the role

HHMI has made a landmark $500 million commitment to support AI-driven projects and 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, which 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.

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, and 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.

Responsibilities

  • 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.

Requirements

  • 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 AlphaFold, 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.
  • Demonstrated innovative research in the application of AI to protein science, structural biology, or related life sciences domains, evidenced by peer-reviewed publication in relevant conferences or journals, contribution of code to high-quality open-source repositories, and/or creation of high-quality applications.
  • Experience applying AI methods to interdisciplinary research, particularly in the biological sciences or related domains, is preferred.
  • Expertise in machine learning with a full understanding of underlying principles and concepts, including supervised and unsupervised learning, deep learning, reinforcement learning, and probabilistic modeling. Recognized as a leader in your area of expertise.
  • Proficiency in AI/ML frameworks and tools such as PyTorch, JAX, or similar.
  • Strong programming and design skills in Python, Julia, C++, or Rust, with experience in developing and optimizing large-scale computational models.
  • Experience with big data technologies and high-performance computing environments.
  • Familiarity with data science techniques, including data preprocessing, statistical analysis, and visualization.
  • Results-oriented with excellent communication skills.

Benefits

  • Competitive compensation package with comprehensive health and welfare benefits.
  • 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.
  • 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 the Washington, DC metro area.
  • Flexible work arrangements.
  • Relocation assistance for non-local candidates transitioning to the Washington, DC metro area.

Pay

HHMI’s salary structure is developed based on relevant market data, considering education, previous experience, knowledge, skills, abilities, and internal equity. Offers typically fall between the minimum and midpoint of the range.

  • AI Scientist I (5+ years’ experience): $182,160.80 (minimum) - $227,701.00 (midpoint) - $296,011.30 (maximum)
  • AI Scientist II (10+ years’ experience): $213,564.00 (minimum) - $266,955.00 (midpoint) - $347,041.40 (maximum)
  • AI Scientist III (15+ years’ experience including program/project management): $245,145.60 (minimum) - $306,432.00 (midpoint) - $450,000.00 (maximum)

This position may also be eligible for incentive pay.

Physical Requirements

  • Remaining in a normal seated or standing position for extended periods.
  • Reaching and grasping by extending hand(s) or arm(s).
  • Dexterity to manipulate objects with fingers, such as using a keyboard.
  • Communication skills using the spoken word.
  • Ability to see and hear within normal parameters.
  • Ability to move about workspace, including moving materials weighing up to several pounds (e.g., a laptop or tablet).

Persons with disabilities may perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

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