ML & Molecular Simulation Scientist

Genesis Molecular AI • San Mateo, CA

1d • Hybrid

About The Position

We are seeking a 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.

Requirements

• 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 Haves

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

Responsibilities

• 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

Benefits

• 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

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree