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Senior Scientist, Computational Protein Engineering

A-Alpha Bio

A-Alpha Bio

Seattle, WA, USA
Posted on Monday, December 11, 2023

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 by combining high-throughput synthetic biology with state-of-the-art machine learning. We partner with leading pharma and biotech companies to enable the discovery of antibodies, molecular glues, and other protein interaction-related drugs. In parallel, we use our AlphaSeq technology internally to build a Biologics Pipeline for clinical development and/or asset licensing opportunities.

Candidates local to Seattle are preferred, but remote applicants are welcome to apply. Candidates must reside in the US.

Starting Salary Range: $145,000 - $176,000 per year

Exemption Status: Exempt

Location Expectations: Remote-Eligible (travel to Seattle required once quarterly, on average)

Role Description

A-Alpha Bio is seeking an accomplished Senior Scientist to lead computational structural biology, combining insights and data from our proprietary high-throughput AlphaSeq platform with state-of-the-art machine learning for protein engineering to deliver high-impact therapeutics.


  • Design, develop, and build a computational platform to predict and refine protein-protein and protein-ligand complexes using quantitative molecular data from AlphaSeq and machine learning.
  • Working alongside bench scientists, establish processes to acquire and curate experimental data for development, validation, and benchmarking of new methods; design synthetic DNA libraries for AlphaSeq to test, inform, and extend modeling results.
  • Work with bench scientists to design, optimize, and test functional antibodies, cytokines, and other biologics as part of A-Alpha’s drug discovery and development pipeline.
  • Engage with global research, industry, and standards development communities to keep abreast of new technologies and best practices, particularly in the fast-moving field of ML for protein structure prediction and protein engineering.



  • Ph.D. in computational chemistry, molecular modeling, structural biology, machine learning, or a related field, with a strong theoretical background as demonstrated by contributions to leading journals; or an equivalent combination of education and experience.
  • 5 or more years of experience in protein structure prediction and analysis, including 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.
  • Hands-on experience designing, training, or utilizing modern deep-learning tools for protein structure prediction or protein engineering (e.g. AlphaFold, ESM, ProteinMPNN, etc.).
  • Excellent programming skills.
  • High level of self-motivation, intellectual curiosity, and eagerness to thrive in a fast-paced, multidisciplinary, and team-oriented start-up environment.


  • Deep technical understanding of targeted protein degradation and/or antibody discovery and optimization.
  • Direct experience with biologics discovery and development in an industry setting.

Candidates of all backgrounds and experience levels are encouraged to apply. Each application will be evaluated on a case-by-case basis.

We offer competitive compensation, including benefits and equity in a fast-growing start-up. Applicants must have legal authorization to work in the United States. At this time, A-Alpha Bio is unable to offer visa sponsorship in any form.

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 scientists. 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 shares our values of speaking the truth, shooting for the moon, taking the reins, playing for the team, and improving the world.

A-Alpha Bio is headquartered in a brand-new combined office/lab space in downtown Seattle's Belltown neighborhood. 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, amateur chefs, explorers, sports fans, bakers, crafters, photographers, brewers, jetsetters, animal lovers, and artists. Whatever your passions, you belong at A-Alpha Bio.