Protein AI Designer - Antibody Sequence Optimization

$165,000 - $205,000

Full-time / Onsite

About The Role

Aequita Bioworks is a biotechnology company using artificial intelligence to develop new monoclonal antibody therapies. We are seeking a highly effective, motivated protein designer to join our Antibody Engineering team. You will partner with research staff to design, implement, and optimize our in-silico protein models.

We are looking for someone who is excited about the promise of artificial intelligence in synthetic biology. If you play with alphafold in your free time, have strong opinions about in-silico modelling of binding affinity, and work with Python on a daily basis you are in the right place!

What You’ll Do

• Utilize state-of-the-art protein language models (LLMs) and machine learning techniques to analyze and optimize antibody sequences
• Carry out humanization, liability remediation, and other biophysical property improvement and/or affinity tuning of large molecules utilizing rational in-silico design approaches
• Develop and refine computational models to predict the impact of sequence modifications on antibody affinity, stability, immunogenicity and manufacturability
• Integrate structural biology data, such as protein-protein interactions and conformational changes, into AI models to enhance prediction accuracy
• Design and implement evaluation methods for competing biological modeling approaches
• Estimate runtime and cost of large scale inference jobs on various compute architectures (e.g. public cloud vs. in house cluster)
• Collaborate with experimental scientists to validate model predictions and refine AI models based on experimental feedback
• Collaborate with the production team to ensure that optimized sequences meet manufacturability standards, including expression levels and purification efficiency
• Stay current with the latest advancements in protein language models, machine learning, and computational biology via paper reading, lab meetings, and conferences.

Who You Are

• PhD in bioengineering, computer science, math, biophysics, computational biology, bioinformatics, chemical engineering, computational biochemistry or related field OR Masters plus 5 years additional postgraduate or industry relevant experience
• Broad knowledge of state-of-the-art machine learning approaches to protein design and biological data analysis
• Familiarity with recent literature and state-of-the-art for large model architectures and training approaches
• Proficient in antibody engineering, including experience with antibody variable domain reformatting, humanization, sequence liability remediation, and/or biophysical property improvement
• Experience with high-throughput screening data and techniques for protein characterization
• Fluency with Python
• Expertise in best practices for software development, including version control, code reviews, unit testing, and CI/CD

Nice to Haves

• Knowledge and hands-on experience with physics-based protein modeling and design methods
• Familiarity with at least one type of molecular modeling software such as Rosetta, Schrodinger, Molecular Operating Environment (MOE)
• Hands-on wet-lab experience in protein sciences or experience working closely with experimentalists strongly preferred
• Experience running large-scale, parallelized bioinformatics pipelines on public cloud or academic HPC clusters

Life at Bioworks 

• Comprehensive Health Coverage – Medical, dental, and vision insurance to keep you at your best
• Financial Security – 401(k) with company matching and fully covered life insurance
• Time to Recharge – Unlimited PTO, generous company holidays, and flexibility to take the time you need
• Wellness First – Group activities, mindfulness sessions, and fitness perks to support your well-being
• Connection & Community – Team lunches, office hangouts, and offsite meetups to build meaningful relationships
• High-Impact Work – Shape the future of digital healthcare at a pivotal moment in our growth
• Competitive Compensation – Top-tier salary and a generous equity package
• Fast-Paced & Exciting – Join a hypergrowth team that moves fast and builds with purpose
• World-Class Team – Work alongside top researchers, scientists, and engineers in a high-performance environment
• Prime Location – Enjoy a sunny workspace in San Carlos

The compensation for this position ranges from $165,000 to $205,000 per year, in addition to benefits. The pay range listed in each job posting represents the minimum and maximum targets for new hire compensation across all locations. Actual pay within this range is determined by factors such as job-related skills, experience, relevant education or training, and location.