Senior Scientist, AI Protein Design

Ampersand Biomedicines is a Flagship Pioneering company on a mission to transform patients’ lives with programmed medicines that work precisely where needed, and nowhere else. We’re building a collaborative, mission-driven team that thrives in a fast-paced environment and shares a genuine desire to make a difference. At Ampersand, employees are encouraged to explore breakthrough science, take chances, support one another, and contribute ideas and perspectives openly.

We are seeking a creative and motivated scientist with expertise in machine learning-driven antibody binder design to join Ampersand’s Computational Science team. This role demands a strong foundation in machine learning/deep learning and sequence/structure-based protein design.

As a Senior Scientist Machine Learning, you will be responsible for developing the frameworks and core models that propel our antibody design process forward. This is an opportunity to be part of a cutting-edge biotech company at the forefront of computational antibody design. You will play a pivotal role in shaping our AND-Body platform, working closely with expert biologists, protein scientists, and computational biologists to push the boundaries of antibody discovery.

To facilitate interactions with other team members and to make the most significant impact on our scientific endeavors, this position requires full-time, on-site presence. We are currently located in South Boston, and will be moving to Watertown summer of 2026.

• Design and conduct independent machine learning research to promote antibody binder design.
• Deliver robust, production-quality models that will drive the next generation of antibody design, advancing both engineering and de novo
• Collaborate closely with experimental teams to align with their capabilities, thereby enabling the creation of advanced hybrid platforms.
• Communicate insights and conclusions to colleagues in the scientific and leadership teams.
• Manage members of the Machine Learning team to drive advancements in our AND-Body platform.
• Develop a high-performing and ambitious team by providing mentorship, growth opportunities, and clear career development pathways for direct reports.
• Foster a culture of collaboration and accountability through strong cross-functional communication, ensuring alignment with key stakeholders and driving business success.
• Contribute to building a positive, team-oriented biotech culture.

• A PhD in biochemistry, biophysics, computational chemistry, computational biology, computer science, machine learning, or a related discipline solving biological or chemical problems using computational approaches.
• 3+ years of industry experience in machine learning/deep learning, modeling, simulation, and design, particularly in sequence and structure-based protein design.
• Experience in leading and managing projects to ensure protein design relevant objectives are met on time and in high quality.
• Demonstrated experience with the state-of-the-art suite of tools for protein design and machine learning approaches (Alpha Fold, ESM, Protein
  
  MPNN, RF-Diffusion, Rosetta, etc)
• Demonstrated experience in the Python programming language in addition to standard machine learning tools (PyTorch, Tensor Flow, JAX, PyG, PyMC, etc).
• Experience with developing novel AI, structure, or sequence-based methods for biomolecular design.

• 3+ years of industry experience that includes significant work in antibody binder AI/ML design.
• Strong communication skills, with the ability to translate complex computational findings into actionable insights within a collaborative group setting.
• Experience working in an interdisciplinary environment, effectively collaborating with bench scientists, with the ability to think independently and contribute to a dynamic intellectual environment.
• Proven track record of successfully managing projects with multiple team members, and monitoring project progress as well as proactively resolving any issues to ensure successful outcomes.
• Expertise with common software development tools and best…