Scientist III Protein Binding Screening & Prediction

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The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

Join our Artificial Intelligence-Powered Lab (AIPL), an initiative at the intersection of academic creativity and start-up style execution. Our mission is to apply machine learning to biological design. Join us as we build a series of interconnected design-test-loop “flywheels” that enable design of synthetic enhancers, protein binders, and more.

AIPL is looking for a scientist to lead our protein binder flywheel. The binder flywheel team is part of a larger effort that includes a total of three experimental flywheel teams and one machine learning team, and that will report into the Sea Hub administrative unit. The goal of the binder flywheel is to produce a model that can accurately predict the effect of amino acid substitutions on the binding of proteins to other proteins, small molecules, and nucleic acids.

To lead this flywheel team, you will need a strong background in protein library screening, protein binder design, or prediction of protein interactions with other molecules. You will lead your team and interact with other team leads, including machine learning colleagues, to optimize active learning processes in your flywheel. You will optimize your flywheel’s turn-around-time and per-cycle model improvement, racing to deliver the best possible ML models for predicting the impact of mutations on protein binding.

You will need a high degree of emotional intelligence, a collaborative mindset, and an ability to work cross-functionally with other research teams to drive project success.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

• Lead the Protein Binder Flywheel team to build and run a rapid, repeatable design–test–learn pipeline focused on protein binding
• Design and oversee protein library screening and binder evaluation experiments to generate high-quality, model-ready datasets
• Partner with machine learning colleagues to define prediction targets, curate/structure data, and implement active-learning strategies that choose the next best experiments
• Optimize flywheel performance by improving turnaround time, throughput, cost, and per-cycle model lift; identify and remove experimental bottlenecks
• Coordinate closely with other flywheel leads and AIPL stakeholders to align priorities, timelines, and dependencies across the broader program
• Mentor and manage a high-performing team, fostering a collaborative culture and clear communication grounded in strong emotional intelligence
• Present scientific results and complex concepts internally in talks and progress reports
• Present results to the external community at conferences and in publications

Note:

Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

• PhD degree in biochemistry, molecular biology, or a related field; or equivalent combination of degree and experience
• Minimum 5 years of relevant post-doctoral experience
• Experience with protein library screening workflows (e.g., yeast/phage display +…