Research Scientist, AI Research

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Job Description

Objective / Purpose:

The global computational chemistry team at Takeda is seeking an exceptional scientist is seeking a Research Scientist to help shape the future of AI-enabled drug discovery at Takeda, with a focus on induced-proximity therapeutics and structure-guided small-molecule design. Working across AI/ML, structural biology, and medicinal chemistry, you will develop cutting-edge computational approaches to explore chemical space more effectively and translate scientific advances into life-saving therapeutic impact.

Accountabilities:                                                                                                      

• Modeling & GenAI
  • Train/finetune diffusion, transformer, and equivariant GNN models for pocket-aware ligand design, pose/affinity prediction, and sequence/structure tasks (co-folding, multimer/ternary modeling).
• Pipelines & Scale
  • Build end-to-end, reproducible pipelines for MSA/co-folding feature generation, data QC, training, and evaluation with experiment tracking; accelerate on multi-GPU/HPC and cloud.
  • Automate large-scale ligand/mutation screening with geometry/covalency checks, pose-quality assessment, and multi-model consensus ranking.
• Physics + AI
  • Integrate docking/MD/MM/GBSA or related physics-based components with learned models to improve prioritization for peptides and small molecules.
• Data & Benchmarking
  • Curate complex structural and proteomics datasets; design retrospective/prospective benchmarks and report robust metrics.
• Productization & Collaboration
  • Package models as services/containers; deliver intuitive analysis apps/dashboards (e.g., Streamlit) and visualizations (e.g., PyMOL integrations).
  • Partner with medicinal chemists, structural biologists, and data scientists; plan experimental validation and communicate decisions clearly.
• Impact & Visibility
  • Contribute to internal methods notes; author publications/posters for leading ML and scientific venues.

Education & Competencies (Technical and Behavioral):

Minimum Qualifications

• PhD in Computer/Data Science, Computational Chemistry/Biology, Chemical Engineering, Biophysics, or related field.
• Demonstrated scientific originality and impact, evidenced by first-author publications in high-impact journals or top-tier ML conferences.
• Hands-on with diffusion models, GNNs/CNNs, transformers, and 3D/structure-aware modeling and finetuning.
• Hands-on experience with Schrödinger (Maestro, LiveDesign) and scripting to automate their use, ideally in a High-Performance Computing (HPC) environment.

Preferred Experience

• Develop and benchmark structure-aware generative models for pocket-conditioned design across synthesizable, billion-scale chemical libraries.
• Experience with parameter-efficient fine-tuning (LoRA / low-rank adapters) of biomolecular foundation models.
• Experience with water/metal site prediction to improve docking/scoring is a plus.
• Experience deploying multi-property generative AI models as containerized REST services (FastAPI, Docker) covering ADMET properties (Lipinski, BBB, CYP, hERG) for medicinal chemistry workflows.
• PhD-level background in all-atom molecular dynamics simulations (LAMMPS, GROMACS, OpenMM) with automated high-throughput workflow management.
• Direct collaboration with medicinal chemistry teams in a pharmaceutical R&D setting, including delivery of ML predictions into production decision-support workflows.
• TPD domain exposure (e.g., CRBN glues, E3 recruitment) and ternary complex or PPI modeling.

Takeda Compensation and Benefits Summary

We understand compensation is an important factor as you consider the next step in your career. We are committed to equitable pay for all employees, and we strive to be more transparent with our pay practices. 

For Location:

Boston, MA

U.S. Base Salary Range:

$116,000.00 - $182,270.00

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location. 

U.S. based employees may be eligible for short-term and/ or long-term incentives. U.S. based employees may be eligible to participate in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and well-being benefits, among others. U.S. based employees are also eligible to receive, per calendar year, up to 80 hours of sick time, and new hires are eligible to accrue up to 120 hours of paid vacation. 

EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.

Locations

Boston, MA

Worker Type

Employee

Worker Sub-Type

Regular

Time Type

Job Exempt

Yes

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.