ML & Molecular Simulation Scientist

Responsibilities

• Build and apply ML models informed by 3D structural data, including geometric deep learning, equivariant neural networks, and diffusion-based generative models.
• Integrate physics-based and ML approaches, combining force field methods and quantum chemistry with modern ML to improve accuracy.
• Develop and apply simulation methods including molecular dynamics, enhanced sampling, and free energy calculations (FEP/TI).
• Contribute to the GEMS platform by improving generative AI, scoring capabilities, and next-gen force fields.
• Collaborate directly with CADD and discovery scientists to apply computational methods from target analysis through lead optimization.
• Communicate scientific results clearly to multidisciplinary teams of chemists and biologists.

Requirements

• PhD in Computer Science, Machine Learning, Chemical Engineering, Biophysics, Physics, or a closely related field.
• Practical experience with 3D machine learning, such as geometric deep learning, graph neural networks, or equivariant architectures.
• Deep, hands-on expertise in molecular simulation (MD, enhanced sampling) using tools like GROMACS, AMBER, OpenMM, or NAMD.
• Proficiency in Python and scientific computing libraries including PyTorch, JAX, NumPy, MDAnalysis, or RDKit.
• Familiarity with structure-based drug design workflows, including docking and protein-ligand interaction modeling.
• Experience working with HPC environments and large-scale simulation workflows.

Preferred Qualifications

• Familiarity with cheminformatics and ADMET property prediction.
• Contributions to open-source simulation or machine learning tooling.
• Postdoctoral or industry experience in a drug discovery setting.

Benefits

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

About the Company

Genesis Molecular AI is pioneering foundation models for molecular AI to unlock a new era of drug design and development. Our platform, GEMS, integrates AI and physics to generate and optimize drug molecules. Genesis is backed by premier investors including a16z, NVIDIA, and Menlo Ventures.