Molecular AI Scientist: Structure-Based Drug Design

USA - 3316 Takeda Development Center Americas, Inc.; Cambridge (MA); On-site; USD 116,000 - 182,000; Full time

Job summary

Takeda in Boston, MA seeks a Research Scientist to advance AI-enabled drug discovery with a focus on structure-guided small-molecule design. You will work across AI/ML, structural biology, and medicinal chemistry to develop computational methods that explore chemical space and translate insights into therapies.

You will build and benchmark advanced ML models, collaborate with multidisciplinary teams, and contribute to internal talks and publications.

Qualifications

• Ph.D. in Computational Biology, Biophysics, Computer Science, Computational Chemistry, or a related field, with a research focus in ML for molecular modeling.
• Hands-on experience developing, training, and validating deep learning models, including architectures relevant to structural biology and chemistry.
• Direct experience with modern structure prediction or co-folding methods (AlphaFold2/3, RoseTTAFold, Boltz) or comparable molecular ML systems.

Responsibilities

• Develop and iterate on deep learning models across the molecular modeling stack: structure prediction, protein-ligand co-folding, affinity, and/or generative design.
• Design and execute benchmarking and evaluation pipelines connecting offline metrics to real-world performance.
• Partner with senior scientists and engineers to integrate models into production-ready workflows.
• Apply computational methods to structural and sequence datasets to guide model development.
• Apply generative AI and predictive ML to design and prioritize chemical matter for projects.
• Communicate findings through talks, write-ups, and publications.

Skills

Deep learning

Python

PyTorch

JAX

Structure prediction

Experiment design

Education

PhD in Computational Biology/ Biophysics/ CS/ Computational Chemistry

Tools

AlphaFold2/3

RoseTTAFold

Diffusion models

GCP/AWS/Azure

Job description

Takeda in Boston, MA seeks a Research Scientist to advance AI-enabled drug discovery with a focus on structure-guided small-molecule design. You will work across AI/ML, structural biology, and medicinal chemistry to develop computational methods that explore chemical space and translate insights into therapies.

You will build and benchmark advanced ML models, collaborate with multidisciplinary teams, and contribute to internal talks and publications.