Scientist III – Protein Binding Screening & Prediction

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 SeaHub 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.

Essential Functions

• 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.

Required Experience and Education

• 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 + FACS/NGS or other high-throughput binder discovery platforms)
• Proven ability to lead scientific projects and collaborate cross-functionally, including partnering effectively with computational/ML teammates

Preferred Education and Experience

• 5 – 8 years relevant post-doctoral experience
• Experience designing or optimizing protein binders and characterizing binding (e.g., affinity/specificity) to proteins, small molecules, or nucleic acids
• Experience building or operating data-driven/active-learning experimental loops and translating assay outputs into model-ready datasets
• Experience with protein engineering/interaction prediction approaches and modern analysis pipelines (e.g., sequence-to-function modeling, structural modeling, or high-throughput data QC/processing)
• Experience with functional genomics, massively parallel reporter assays, multiplexed assays of variant effect, saturation mutagenesis, or plasmid library-based screening
• Experience performing molecular biology methods including library cloning, Golden Gate assembly, Gibson assembly, CRISPR/Cas9-editing, mammalian cell culture, stem cell culture, and NGS library prep

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment

Work Environment

• Frequently required to sit, stand, walk, stoop, kneel or reach
• Possible exposure and handling of laboratory animals
• Laboratory atmosphere - possible exposure to chemical, biological or other hazardous substances

Position Type/Expected Hours of Work

• This role is currently working onsite and is expected to work onsite for the majority of the working hours. We are a Washington State employer, and the primary work location for Allen Institute employees is 700 Dexter Ave N.; any remote work must be performed in Washington state

Travel

• The successful candidate may be invited to attend occasional national and international conferences

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer work visa sponsorship**

Annualized Salary Range

• $128,050 - $160,050

* Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.