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Protein Simulation Jobs (NOW HIRING)

Battelle

Computational Biologist

Columbus, OH · On-site

Molecular dynamics simulations and structure based optimization * Integration of AI/ML tools for protein design and optimization * Development and maintenance of reproducible computational protein ...

Achira

CADD / Application Scientist

New York, NY · On-site

$164K - $259K/yr

... simulation that can make the chemical and biological systems behind drug discovery more learnable, predictable, and designable. You will be part of the journey from our first protein-ligand ...

Achira

CADD, Application Scientist

Manhattan, NY · On-site

... simulation that can make the chemical and biological systems behind drug discovery more learnable, predictable, and designable. You will be part of the journey from our first protein-ligand ...

Harvard University

Postdoctoral Fellow

Cambridge, MA · On-site

$54K - $73K/yr

G-protein-coupled receptors (GPCRs); Cell and molecular biology -Cryo-vitrification via cryo-plunging and high-pressure freezing; Time-resolved freezing -Microfluidics; design, simulation ...

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Protein Simulation information

See salary details

$39K

$123.4K

$190.5K

How much do protein simulation jobs pay per year?

As of Sep 11, 2026, the average yearly pay for protein simulation in the United States is $123,399.00, according to ZipRecruiter salary data. Most workers in this role earn between $92,000.00 and $146,500.00 per year, depending on experience, location, and employer.

What is the difference between Protein Simulation vs Molecular Dynamics Specialist?

AspectProtein SimulationMolecular Dynamics Specialist
Required CredentialsDegree in Biochemistry, Bioinformatics, or related field; knowledge of simulation softwareDegree in Chemistry, Physics, or related; expertise in molecular dynamics tools
Work EnvironmentResearch labs, pharmaceutical companies, academic institutionsResearch labs, biotech firms, academic research centers
Industry UsageUsed for studying protein behavior, drug design, and structural analysisFocuses on running and analyzing molecular dynamics simulations

Protein Simulation involves creating computational models of proteins to study their structure and function, often using specialized software. A Molecular Dynamics Specialist specializes in executing and analyzing molecular dynamics simulations, which are a subset of protein modeling techniques. While both roles require similar educational backgrounds and are used in research and biotech industries, Protein Simulation is broader, encompassing various modeling approaches, whereas Molecular Dynamics Specialists focus specifically on dynamic simulation techniques.

What other helpful pages are available for Protein Simulation?

Other pages related to Protein Simulation:

Infographic showing various Protein Simulation job openings in the United States as of September 2026, with employment types broken down into 100% Full Time. Highlights an 100% In-person job distribution, with an average salary of $123,399 per year, or $59.3 per hour.

ML & Molecular Simulation Scientist

San Mateo, CA • On-site

Genesis Molecular AI
See more jobs at Genesis Molecular AIexternal

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted yesterday

Key responsibilities

  • Develop and apply methods at the intersection of 3D molecular simulation and machine learning to support drug discovery programs.

  • Build and implement ML models informed by 3D structural data, including geometric deep learning, equivariant neural networks, and diffusion-based generative models.

  • Design, run, and improve simulation methods such as molecular dynamics, enhanced sampling, and free energy calculations to aid active drug discovery efforts.

Job description

About the Team
At Genesis Molecular AI, we're a tight-knit team 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 don't just apply machine learning to biology - we conduct fundamental research at the intersection of machine learning, physics, and computational chemistry, pushing the boundaries of each field.
At Genesis, simulation and machine learning aren't separate disciplines: they're deeply integrated, and the scientists who do this work 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 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

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 into industry-leading models to generate and optimize drug molecules, including the breakthrough generative diffusion model Pearl for structure prediction. Genesis is backed by premier AI and life science investors, including a16z, NVIDIA, Rock Springs Capital, Menlo Ventures, T. Rowe Price, Fidelity, and Radical Ventures. Genesis has also signed category-leading AI-pharma deals, the most recent of which was a significant expansion with Incyte (see coverage in Forbes and GEN) with a total potential deal value of several billion dollars.
Genesis is headquartered in San Mateo, CA, with a fully integrated laboratory in San Diego. We are proud to be an inclusive workplace and an Equal Opportunity Employer.

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