Postdoctoral Research Fellow, Protein Design

Visterra; Waltham (MA); On-site; USD 80,000 - 120,000; Full time

Job summary

Visterra seeks a creative Postdoctoral Research Fellow for the Protein Design team to shape early-stage drug discovery by applying cutting-edge protein design and machine learning methods to therapeutic challenges. You will work with antibody and non-antibody biotherapeutics, collaborating across computational and experimental groups.

The role is based in Visterra's Waltham, MA offices, with an expected 24-month fellowship length and a focus on advancing ML-driven structure prediction and de

Qualifications

• This is a Ph.D.-level research role requiring extensive protein design experience.
• Strong knowledge of experimental and computational protein structure/function and engineering.
• Experience employing or developing protein design methods.
• Proficiency with Python and machine learning frameworks for data analysis.

Responsibilities

• Champion the integration of cutting-edge ML methods into protein design workflows.
• Collaborate with computational and experimental scientists to drive design of therapeutic proteins and antibodies.
• Analyze results, troubleshoot methods, and propose creative solutions.
• Translate complex data analyses into clear findings for colleagues and leadership.
• Contribute to publication of novel methods and research findings.

Skills

Python

ML libraries

Education

Ph.D. or equivalent in computational/structural biology/biochemistry

Tools

PyRosetta

AlphaFold

ESMFold

RFdiffusion

ProteinMPNN

BindCraft

PyMOL

Job description

The Opportunity

Visterra is seeking a creative and driven Postdoctoral Research Fellow to join our Protein Design team. This is an exciting, hands‑on opportunity to shape early‑stage drug discovery programs across a broad portfolio, working with a team that gives you the resources and scale to put your ideas to the test. In this role, you will bring cutting‑edge protein design approaches directly into our pipeline, building and applying machine learning methods for structure prediction, de novo protein and antibody design, and computational optimization to tackle real therapeutic challenges.

Reporting to the Associate Director, Research, the ideal candidate is highly motivated, eager to learn, intellectually curious, and deeply collaborative, with the drive to thrive in a fast‑paced, interdisciplinary environment. It is an excellent opportunity to join a team with deep experience in protein design and gain hands‑on experience working across both antibody and non‑antibody based biotherapeutics.

This is a full‑time position located at Visterra’s offices in Waltham, MA. The expected length of the fellowship is 24 months.

Responsibilities

• Champion the integration of the latest machine learning methods and emerging technologies into our protein design workflows.
• Stay ahead of the field. Read broadly, evaluate new tools critically, and bring the best ones in‑house.
• Partner with computational and experimental scientists inside and outside Visterra to drive structure- and property‑guided design of therapeutic proteins and antibodies.
• Dig into scientific results, troubleshoot methods, and invent creative solutions to complex challenges.
• Translate complex data analyses into clear, compelling findings and communicate them confidently to colleagues and leadership.
• Bring fresh ideas to team meetings and actively push programs forward throughout the drug discovery process.
• Potential opportunities to publish novel methods and research findings at conferences and in scientific journals.

Requirements

• A Ph.D. or equivalent in computational biology, structural biology, biochemistry, or a related discipline with significant and extensive experience in protein design.
• Strong knowledge of the experimental and computational aspects of protein structure/function and engineering.
• Demonstrated track record of employing or developing protein design methods.
• Proficient in tools/algorithms used for computational modeling, design and analysis of proteins (e.g., PyRosetta, AlphaFold, ESMFold, and related structure predictors, RFdiffusion, ProteinMPNN, BindCraft, and related protein design tools, PyMOL, etc.).
• Hands‑on experience with processing and analysis of large and complex datasets.
• Highly proficient with Python and Python libraries for data analysis, machine learning and deep learning frameworks.
• Experience working in a Linux environment, including bash scripting.
• Comfortable working in high‑performance computing (e.g., SLURM) and/or cloud environments.
• Ability to work in multi‑disciplinary teams, displaying excellent interpersonal skills.
• Ability to help direct experimental evaluation of computational methods and/or designs, and to use experimental data to validate and refine in silico methods.

Travel

Possible travel to local and national conferences.

Job Type

Full time, temporary with fixed term.

About Visterra

Visterra is a biotechnology company focused on discovery, pre‑clinical research and clinical trial material manufacturing of biologic therapeutic candidates. We are committed to developing innovative protein‑based therapies for the treatment of patients with kidney, immune‑mediated and other hard‑to‑treat diseases. We have a robust pipeline of discovery and preclinical‑stage programs. Several Visterra‑originated assets are being studied in clinical trials by our affiliates or partners and one asset, VIS649 (sibeprenlimab), has received FDA approval.

Visterra is an indirect wholly‑owned, independent operating subsidiary of Otsuka Pharmaceutical Co., Ltd., a global pharmaceutical and nutraceutical company headquartered in Japan. As a member of the Otsuka family of companies, we are uniquely positioned as a small, nimble and innovative organization where individuals and teams are empowered to make big impacts – while benefiting from the support, strength, stability and long‑term perspective of a 100‑year‑old global company. We have approximately 100 employees and are located in Waltham, Massachusetts. For more information, please visit visterrainc.com.

Salary range: $80,000 - $120,000

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.