Location: Seattle preferred but open to remote

A-Alpha Bio Summary

A-Alpha Bio is an early stage and rapidly growing drug discovery company headquartered in Seattle, WA. We are enabling the next generation of high-impact therapeutics with synthetic biology and machine learning. We partner with leading pharma and biotech companies to enable the discovery of antibodies, molecular glues, and other protein interaction-related drugs.

Role Description

We are seeking an accomplished Scientist or Senior Scientist to lead computational molecular modeling, combining insights from computational structural biology with data from our proprietary high-throughput AlphaSeq platform to deliver high-impact therapeutics.  


  • Design, develop, and build a computational modeling/simulation platform to study protein structure and dynamics, antibody-antigen and other protein-protein interactions, as well as protein-small molecule interactions
  • Working alongside bench scientists, establish processes to acquire and curate experimental data for development, validation, and benchmarking of new methods; design and synthetic DNA libraries for AlphaSeq to test, inform and extend modeling results
  • Work with Data Scientists and Machine Learning Scientists at A-Alpha to develop additional computational approaches (e.g. bioinformatics, machine learning) to augment computational chemistry approaches
  • Engage with global research, industry, and standards development communities to keep abreast of new technologies and best practices


  • A completed Ph.D. in computational chemistry, molecular modeling, structural biology, or related field with strong theoretical background as demonstrated by contributions to leading journals
  • At least 3 years of experience directly applied to problems in the Biotech/Pharmaceutical sector
  • Solid background in protein structure and experience in tools for protein analysis/design such as Rosetta, Schrodinger, MOE, including relevant Molecular Dynamics packages.
  • Strong programming skills (e.g. R, Python, or C++). Ability to work in both Windows and Unix.
  • Impressive track record of publications/accomplishments in computational structural biology at top-tier academic institutions or companies
  • Must be highly self-motivated, intellectually curious, and excited to thrive in a fast-paced, multidisciplinary, and team-oriented start-up environment

Preferred Qualifications

  • Expert knowledge of modern computational chemistry packages and tools, with an emphasis on molecular dynamics, structure prediction and analysis, virtual screening/docking, and free energy determination
  • Deep technical understanding of targeted protein degradation and/or antibody discovery and optimization
  • Experience with deep learning

We offer competitive compensation including a pay package, benefits, and equity in a fast-growing start-up. Job title will be set based on experience and track record, so we encourage applicants with a wide range of backgrounds to apply.  

About A-Alpha Bio

A-Alpha Bio is an early-stage biotechnology company combining synthetic biology and machine learning to dramatically improve the discovery of high-impact therapeutics. We believe that abundant high-quality data is critical for understanding biology and curing disease – and synthetic biology is our catalyst. Our proprietary AlphaSeq platform uses genetically engineered cells to quantitatively measure millions of protein interactions – from which we generate high-resolution models of biology.

In 2018, we spun out of the University of Washington’s Institute for Protein Design and Center for Synthetic Biology – both fantastic communities of brilliant and highly entrepreneurial scientist. Initial financial support came from the National Science Foundation, Bill & Melinda Gates Foundation, and a seed round in September 2019 led by OS Fund. Since the company’s inception, we have focused on partnering with pharmaceutical companies to discover and optimize drugs for therapeutic areas ranging from infectious disease to cancer. We are growing rapidly, and new members of the team should expect a fast-paced and highly dynamic work environment. We are building a diverse, meritocratic, and supportive team that values hard work, creativity, transparency, individual and team growth, flexibility, and kindness.

A-Alpha Bio is headquartered in Seattle at Fluke Hall, a startup incubator operated by the University of Washington (although, we will be moving soon!). While the startup lifestyle occasionally requires grueling hours, we strongly value the need for a work-life balance and time out of the lab/office. We are fortunate to be situated in a region that is renowned for its premier outdoor activities, including hiking, biking, climbing, skiing, kayaking, and sailing. At A-Alpha, you’ll find many who love the outdoors, but also gamers, bakers, photographers, brewers, jetsetters, animal lovers, and artists. Whatever your passions, you belong at A-Alpha Bio.

Apply for this Job

* Required
When autocomplete results are available use up and down arrows to review
+ Add Another Education