Scientist, Antibody Design and Protein Engineering

Summary:

Visterra is seeking a highly talented and motivated Scientist to join our Protein Design and Modeling group, reporting to the Sr. Director of Research. This role focuses on leveraging and advancing cutting-edge methods for the design of novel therapeutics. The successful candidate will contribute to challenging design initiatives and collaborate closely with both computational and experimental scientists to develop, refine, and deploy tools for structure prediction, protein engineering, and data analysis. Candidates should have a strong foundation in protein engineering and a demonstrated ability to utilize modern protein design and modeling technologies. We’re looking for someone who is driven, intellectually curious, a critical thinker, and thrives in a collaborative, interdisciplinary environment. This is a full-time, in-office position located at Visterra’s offices in Waltham, MA.

Key duties and responsibilities:

• Develop, implement, and apply innovative deep learning and AI-based methods for protein structure prediction, design, and optimization.
• Evaluate and implement emerging computational tools, algorithms, and best practices in the field of machine learning-driven protein engineering.
• Integrate computational modeling and advanced analytics with experimental workflows to design and optimize antibodies and other therapeutic proteins.
• Collaborate closely with other computational and experimental scientists to support iterative design of therapeutic proteins and antibodies.
• Independently analyze scientific results, troubleshoot computational and data-driven challenges, and develop creative solutions and workflows to address challenges.
• Prepare technical documents and deliver clear, effective presentations on project progress, findings, and strategy to internal teams.
• Develop research plans and manage multiple concurrent projects or workflows.
• May include supervision and mentorship of direct reports.

Minimum Qualifications

• A Ph. D. or equivalent in computational biology, bioinformatics, structural biology, or a related discipline with significant and extensive experience in protein design.
• Strong foundation in deep learning, particularly as applied to protein structure modeling (e.g. AlphaFold, ProteinMPNN, RFdiffusion).
• Demonstrated experience applying machine learning to solve real-world problems in protein engineering or design.
• Familiarity with experimental approaches for protein characterization (e.g. expression, purification, biophysics, and binding assays).
• Proficient in Python and deep learning frameworks (e.g. PyTorch).
• Proficient with Linux, including experience using high performance computing environments.
• Ability to work in multi-disciplinary teams, displaying excellent interpersonal skills.
• Exceptional communication skills (written and verbal), with a proven ability to convey complex ideas in a clear, precise, and actionable manner to diverse teams at all levels of the organization.

Preferred Qualifications:

• Experience developing custom ML/AI models for biological sequence or structure generation.
• Experience using Rosetta-based methods for protein design and modeling.
• Prior experience engineering therapeutic antibodies or other biologics.
• Familiarity with cloud computing or GPU-accelerated infrastructure.
• Track record of publications in the field of computational protein design.

Management responsibilities: This position may include supervisory responsibilities

Travel: Possible travel to local and national conferences

Company:

Visterra is a clinical stage biotechnology company committed to developing innova­tive biologic therapies (antibodies and therapeutic proteins) for the treatment of kidney diseases and other hard-to-treat diseases. Our proprietary technology platform enables the design and engineering of precision antibody or protein-based drug candidates to modulate key disease targets. We are developing a robust pipeline of novel therapies for patients with unmet needs.

Visterra is a wholly-owned subsidiary of Otsuka America, Inc., which is a U.S. holding company and a wholly owned subsidiary of Otsuka Pharmaceutical Co., Ltd. of Japan. Visterra has approximately 125 employees and is located in Waltham, Massachusetts.

Visterra provides equal employment opportunities to all employees and applicants for employment and prohibits discrimination and harassment of any type without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws.