Johnson & Johnson Innovative Medicine · 14 hours ago
Senior Scientist, Protein Design
Cambridge, MA
Full-time
Hybrid
Mid, Senior Level
$109K/yr - $175K/yrJohnson & Johnson Innovative Medicine is dedicated to advancing healthcare through innovative solutions. They are seeking a Senior Scientist in Protein Design to lead molecular design and simulation initiatives, supporting drug discovery and development for protein-based therapeutics.
Pharmaceuticals
Responsibilities
Work directly with wet-lab scientists and therapeutic areas to design and optimize protein molecules for specific functions and properties, with a focus on antibody therapeutics
Collaborate with team members across Therapeutics Discovery on the planning, prioritization, and timely delivery of designs to support multiple concurrent programs
Serve as an In Silico Discovery Lead on diverse project teams
Work with ML colleagues to guide development, benchmarking, and application of pioneering generative and discriminative models
Model sophisticated biological systems using a variety of methods and tools to advise design methodology
Participate in internal and external presentations, peer-reviewed manuscripts and conference proceedings
Qualification
Required
PhD in Biomedical Engineering, Biochemistry, Computational Biology, Computer Science, Structural Biology, Biophysics, Material Science, or other related quantitative field required
Advanced experience in computational protein modeling, design, structural biology, and biophysics is required
Ability to lead projects in cross-functional teams to completion in a collaborative manner is required
Experience with antibody and/or nanobody modeling and design is required
Experience with high performance computing (on-prem or cloud) is required
Solid understanding of current machine learning architectures is required
Advanced proficiency in Python and related data-science packages such as Pandas and Numpy is required
Excellent communication, reporting and team interaction skills is required
Desire for continuous learning and the ability to identify, evaluate and deploy emerging algorithms, models, and protein design workflows is required
Experience with powerful ML and biophysics packages for protein modeling and design such as AlphaFold, Boltz2, ESMFold, ImmuneBuilder, ProteinMPNN, RFDiffusion, RFAntibody, Boltzgen, Germinal, Chai-2, Chroma, Rosetta, etc is required
Preferred
Experience in de novo protein design and sophisticated protein design techniques, such as large scale backbone editing is preferred
Knowledge of critical wet-lab techniques used in protein engineering such as yeast display, SPR, ITC, CD-spectroscopy is preferred
Experience using Schrodinger, Discovery Studio, MOE, GROMACS, NAMD or other molecular dynamics simulation software is preferred
Experience with retraining, fine-tuning, and building ML models such as LLMs to support advanced protein design and protein property prediction tools is preferred
Experience mentoring and leading junior scientists is strongly preferred
Benefits
Medical
Dental
Vision
Life insurance
Short- and long-term disability
Business accident insurance
Group legal insurance
Consolidated retirement plan (pension)
Savings plan (401(k))
Vacation – up to 120 hours per calendar year
Sick time - up to 40 hours per calendar year
Holiday pay, including Floating Holidays – up to 13 days per calendar year of Work
Personal and Family Time - up to 40 hours per calendar year
Company
Johnson & Johnson Innovative Medicine
Johnson and Johnson Innovative Medicine focuses on developing medical solutions for some of the challenging diseases and medical conditions.
10001+ employees
Funding
Current Stage
Late StageLeadership Team
Molly Perkins
VP, Head of Cell & Genetic Medicines Discovery
Recent News
2025-08-14
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