Senior Scientist, Computational Biotherapeutics Engineering

About the role

Pfizer’s BioMedicine Design department is seeking a scientist with expertise in computational AI/ML methods spanning protein modeling, representation learning, and generative model development. You will join a computational team working closely with experimental scientists on discovery and optimization of industry-leading biotherapeutics.

Responsibilities

• Implement advanced cutting-edge AI and machine learning workflows for computational protein design (including fine-tuning protein language models and generative protein design) in HPC or scalable cloud computing environments
• Collaborate with machine learning colleagues on the design and training of AI/ML models for antibody developability engineering. Apply these models to optimize leads for antibody drug discovery projects
• Stay informed about developments in NLP, ML, and generative AI to create innovative solutions for molecular discovery, design, and optimization to advance therapeutic discovery and development
• Serve as a technical expert in deep learning models for protein sequence and structure, supporting discovery teams with AI/ML-driven design strategies
• Analyze large-scale sequence, structure, and experimental datasets to learn representations linking protein features to developability and pharmaceutical properties
• Communicate complex scientific ideas, model behavior, limitations, and design recommendations to both technical and non-technical audiences, fostering collaborations across multidisciplinary teams
• Collaborate with computational and wet lab experts to optimize the computational developability platform, offering both individual and team-based innovative solutions

Requirements

• Must-have: PhD in biochemistry, computational chemistry, computational biology, machine learning, or a related field with 0-3 years of experience OR Master's Degree in biochemistry, computational chemistry, computational biology, machine learning with 7-8 years of experience OR BA/BS with 9-11 years of experience
• Demonstrated track record (including publications or equivalent impact) of using AI/ML-driven protein modeling/design to influence project direction and strategy
• Hands-on experience using and interrogating modern AI/ML models for protein representation, structure prediction, or generation (e.g., transformer or diffusion-based approaches)
• Strong understanding of protein structure, sequence-structure relationships, and model evaluation
• Experience programming in Python and using modern scientific or machine learning libraries (e.g., NumPy/SciPy, scikit-learn, PyTorch), including training and evaluation workflows
• Experience working with large biological datasets and bioinformatics resources

Qualifications

• Nice to have: Experience with protein language models (e.g., ESM-family models), generative structure models (e.g., RFdiffusion, BoltzGen, BindCraft), and structural prediction AI models (e.g. AlphaFold)
• Familiarity with equivariant or structure-aware neural networks
• Knowledge of antibody structure, multispecific design, or developability modeling
• Experience running and scaling deep learning workloads on HPC/GPU/cloud environments using technologies such as Slurm, AWS, or Google cloud
• Experience with structure-based molecular modeling software (Rosetta, Schrödinger, MOE, FoldX)

Benefits

The annual base salary for this position ranges from $93,600.00 to $156,000.00. In addition, this position is eligible for participation in Pfizer’s Global Performance Plan with a bonus target of 12.5% of the base salary and eligibility to participate in our share-based long-term incentive program. We offer comprehensive and generous benefits and programs to help our colleagues lead healthy lives and to support each of life’s moments. Benefits offered include a 401(k) plan with Pfizer Matching Contributions and an additional Pfizer Retirement Savings Contribution, paid vacation, holiday and personal days, paid caregiver/parental and medical leave, and health benefits to include medical, prescription drug, dental and vision coverage.