ML & Molecular Simulation Scientist

Genesis Molecular AI; San Mateo (CA); On-site; USD 100,000 - 130,000; Full time

Benefits offered by this job

Highly competitive compensation

Comprehensive health, dental, and vision insurance

401(k) plan

Open PTO policy

Daily meals and snacks

Job summary

Genesis Molecular AI is seeking an ML & Molecular Simulation Scientist to develop methods at the intersection of 3D molecular simulation and machine learning to impact drug discovery programs.

The candidate will work on building ML models informed by structural data and collaborate with teams in drug discovery. The ideal candidate has a PhD and practical experience in molecular simulation using tools like GROMACS.

Competitive compensation and comprehensive health insurance are part of the package.

Qualifications

• Hands-on expertise in molecular simulation methods like MD and free-energy calculations.
• Experience with 3D machine learning methods relevant to molecular data.
• Proficient in computational workflows for drug discovery.

Responsibilities

• Develop and apply ML models informed by 3D structural data for drug discovery.
• Collaborate with scientists to support computational methods across the drug discovery pipeline.
• Stay current with literature on geometric ML and biomolecular simulation.

Skills

3D machine learning

geometric deep learning

molecular simulation

Python

scientific computing libraries

Education

PhD in computer science, machine learning, chemical engineering, biophysics, or physics

Tools

GROMACS

PyMOL

NumPy

Job description

About the Team

At Genesis Molecular AI, we are a tight‑knit group of deep learning researchers, computational scientists, and drug discovery pioneers united by a single mission: to develop the next generation of AI‑driven therapies for patients with severe diseases. We conduct fundamental research at the intersection of machine learning, physics, and computational chemistry, pushing the boundaries of each field. Simulation and machine learning are deeply integrated, and scientists who work here sit at the center of everything we build. You will work side by side with world‑class researchers across ML, chemistry, and biology, with access to large‑scale compute infrastructure and simulation pipelines, contributing to a platform where physics‑based methods and AI advance together.

About the Role

We are seeking an ML & Molecular Simulation Scientist to develop and apply methods at the intersection of 3D molecular simulation and machine learning, and see those methods through to real impact in drug discovery programs.

This is a role for someone who thrives at the intersection of computational science and machine learning: designing and running simulations, building ML models grounded in physical intuition, and collaborating directly with CADD and discovery teams to move molecules from hit identification to lead optimization.

Some areas you may focus on

• Build and apply ML models informed by 3D structural data, including geometric deep learning, equivariant neural networks, and diffusion‑based generative models for molecular design and property prediction
• Integrate physics‑based and ML + data‑driven approaches, combining force‑field methods, quantum chemistry, and structure‑based design with modern ML to improve accuracy and throughput
• Develop and apply simulation methods spanning molecular dynamics, enhanced sampling (metadynamics, replica exchange, umbrella sampling), and free‑energy calculations (FEP/TI) to support active drug discovery programs
• Contribute to the GEMS platform, improving our generative AI and scoring capabilities, focusing on 3D methods; strengthen ML and physics‑based scoring functions (and their intersection), build next‑gen force fields
• Work directly with CADD and discovery scientists to apply computational methods across the drug discovery pipeline, from target structure analysis through lead optimization
• Stay current with the field, implementing and adapting methods from the latest literature in geometric ML, biomolecular simulation, and computational drug design
• Communicate scientific results clearly to multidisciplinary teams, including experimental chemists and biologists

Who You Are

• Practical experience with 3D machine learning – geometric deep learning, graph neural networks, equivariant architectures (e.g., SE(3)/E(3) networks), or diffusion models applied to molecular data
• PhD (preferred) in computer science, machine learning, chemical engineering, biophysics, physics, or a closely related field; postdoctoral or industry experience is a plus
• Deep, hands‑on expertise in molecular simulation, including MD, enhanced sampling, and/or free‑energy methods using tools such as GROMACS, AMBER, OpenMM, or NAMD
• Familiarity with structure‑based drug design workflows: docking, binding‑site analysis, protein‑ligand interaction modeling using tools such as MOE, or PyMOL
• Proficiency in Python and scientific computing libraries (PyTorch, JAX, NumPy, MDAnalysis, RDKit); comfort with HPC environments and scripting for large‑scale simulation workflows
• A track record of applying computational methods to real scientific problems, demonstrated through publications, open‑source contributions, or industry impact
• Collaborative, curious, and able to move between rigorous method development and fast‑paced discovery work

Nice to Have

• Familiarity with cheminformatics and ADMET property prediction
• Contributions to open‑source simulation or ML tooling

What We Offer

• Highly competitive compensation including base, bonus, and equity
• Comprehensive health, dental, and vision insurance (fully covered for employees)
• Stock option eligibility
• 401(k) plan
• Open PTO policy
• Paid company holidays
• Daily meals and snacks in the office
• Flexible work environment

About Genesis Molecular AI

Genesis Molecular AI is pioneering foundation models for molecular AI to unlock a new era of drug design and development. Our generative and predictive AI platform, GEMS (Genesis Exploration of Molecular Space), integrates AI and physics to generate and optimize drug molecules, including the breakthrough generative diffusion model Pearl for structure prediction. Genesis is proud to be an inclusive workplace and an Equal Opportunity Employer.