AI Cheminformatics Engineer I

Frontier Medicines; South San Francisco (CA); On-site; USD 100,000 - 159,000; Full time

Benefits offered by this job

Health Care Plan

401k/IRA

Paid Time Off

Stock options

Training & Development

Free Food & Snacks

Wellness Resources

Job summary

Frontier Medicines seeks a Scientist, AI Engineer to advance AI and cheminformatics for covalent small molecule drug discovery. You will design, train, and deploy multimodal models that leverage proprietary chemistry and proteomics data to accelerate compound design and optimization.

You will collaborate with medicinal chemistry, biology, and cross-functional teams to build AI-powered tools that translate complex data into actionable scientific insight, contributing to a startup-like, highly

Qualifications

• Design architecture and training strategies for domain-specific multimodal AI models.
• Design and build multi-agent systems for scientific research workflows.
• Develop generative molecular design approaches and diffusion models.
• Build multimodal RAG pipelines over structured data and reports.
• Train, evaluate, and deploy deep learning models for molecular property prediction.
• Implement and benchmark molecular representations and transfer learning.
• Deploy models into serving infrastructure for researchers.

Responsibilities

• Design architecture and training strategies for domain-specific multimodal AI models that reason over molecular structures, assay data, protein structures, and scientific text — trained on Frontier’s proprietary data.
• Design and build multi-agent systems for scientific research workflows and tool interfacing.
• Develop and adapt generative molecular design approaches to explore covalent compound libraries.
• Build multimodal RAG pipelines over structured data and experimental reports.
• Train, evaluate, and deploy deep learning models for molecular property prediction and SAR analysis.
• Deploy models into serving infrastructure reachable by researchers and agents.

Skills

Domain multimodal AI

MoE training

Agentic AI systems

Molecule data understanding

Python programming

Collaborative work

Self-supervised learning

Distributed training

Education

B.Sc in computational/quantitative discipline

PhD with industry experience

Tools

DeepSpeed

FSDP

PyTorch

Job description

Frontier Medicines is seeking a highly motivated Scientist, AI Engineer to join our AI organization. This role will play a key scientific and technical role in advancing Frontier’s AI and cheminformatics capabilities in support of covalent small molecule drug discovery.

The successful candidate will design and deploy machine learning models, agentic AI systems, and multimodal foundation and generative models that leverage Frontier's large-scale covalent chemistry and chemoproteomics data to accelerate compound design, prioritization, and optimization. This role works closely with medicinal chemistry, biology, and cross-functional drug discovery teams to build AI-powered tools that translate complex, heterogeneous data into actionable scientific insight

This position is ideal for an individual contributor who thrives in scientifically uncharted territory and enjoys building novel solutions for medicinal chemistry, biology, and computational chemistry teams.

This is an exciting opportunity in our South San Francisco site to deploy AI to make a difference for patients suffering from debilitating diseases by working in a highly collaborative and energetic team in a startup environment with short communication lines across functions and departments

Requirements

What we are looking for:

• Design architecture and training strategies for domain-specific multimodal AI models that reason over molecular structures, assay data, protein structures, and scientific text — trained on Frontier’s proprietary data. Familar with self-supervised learning, and Mixture of experts (MoE) and Distributed training (DeepSpeed, FSDP)
• Design and build multi-agent systems for scientific research workflows — supervisor/sub-agent orchestration, MCPs, task decomposition, tool calling, error recovery, and human-in-the-loop checkpoints that interface with internal systems (scientific databases, compound registries)
• Develop and adapt generative molecular design approaches — diffusion models, autoregressive transformers, VAEs, reinforcement learning–guided generation — to explore and expand covalent compound libraries and novel chemical space.
• Build multimodal RAG pipelines over structured data, slide decks, experimental reports, and images
• Train, evaluate, and deploy deep learning models for molecular property prediction, virtual screening, ADMET modeling, and SAR analysis on Frontier’s covalent chemistry data.
• Implement and benchmark molecular representations — GNNs, equivariant architectures, learned fingerprints — and build multi-task,transfer learning, and active learning approaches that leverage proprietary data for low-data regime predictions on active programs.
• Deploy models into serving infrastructure that researchers and agents can query — endpoints, batch inference, monitoring — so predictions reach decisions.

Traits We Believe Make a Strong Candidate

• B.Sc in computational or quantitative discipline such as computer science, data science, cheminformatics, computational chemistry or related field with 2-3 years industry experience.
• Strong programming skills in Python and experience with coding tools.
• Ability to work independently while thriving in a highly collaborative, cross-functional environment.
• Excellent written and verbal communication skills.
• Legally authorized to work in the United States.

Leveling Guidelines

Scientist I

• Education & Experience:
• Bachelor’s degree with 2–3 years of relevant industry experience, or
• PhD with at least 1 year of relevant industry experience

Demonstrated ability to independently or with limited guidance design and execute computational and AI approaches for drug discovery problems Proven track record of contributing to complex analytical strategies and influencing discovery programs through data-driven insights Ability to effectively collaborate with experts across disciplines and contribute to cross-functional team success

Benefits

• Health Care Plan (Medical, Dental & Vision)
• Retirement Plan (401k, IRA)
• Life Insurance (Basic, Voluntary & AD&D)
• Paid Time Off (Vacation, Sick & Public Holidays)
• Family Leave (Maternity, Paternity)
• Short Term & Long Term Disability
• Training & Development
• Free Food & Snacks
• Wellness Resources
• Stock Option Plan

At Frontier, we strive to build a diverse and equitable workplace. The salary range for this role is $100,000 - $158,900. Compensation for the role will depend on a number of factors, including candidates' qualifications, skills, competencies and experience. Frontier offers a competitive total rewards package which includes healthcare coverage, 401k and a broad range of other benefits.

This compensation and benefits information is based on Frontier's knowledge as of the date of publication, and may be modified in the future.