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Molecular Dynamics Jobs (NOW HIRING)

1910

Computational Theoretical Chemist I

Boston, MA

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulations are changing the way we develop new drugs. At 1910 , we put computation at the ...

UAB

SCIENTIST III

Tampa, FL

The role requires deep technical expertise across AI for science protein and antibody design, AI-driven molecular dynamics, agentic AI and autonomous research systems, clinical trial simulations ...

UAB NOVA RENT

SCIENTIST III

Birmingham, AL · On-site

The role requires deep technical expertise across AI for science protein and antibody design, AI-driven molecular dynamics, agentic AI and autonomous research systems, clinical trial simulations ...

1910

Computational Theoretical Chemist I

Boston, MA · On-site

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulations are changing the way we develop new drugs. At 1910 , we put computation at the ...

1910

Computational Theoretical Chemist II

Boston, MA · On-site

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulation are changing the way we develop new drugs. At 1910 , we put computation at the heart ...

1910

Computational Theoretical Chemist I

Boston, MA

Advances in big chemical data, massive computing power, artificial intelligence, and molecular dynamics simulations are changing the way we develop new drugs. At 1910 , we put computation at the ...

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How much do molecular dynamics jobs pay per year?

As of Aug 16, 2026, the average yearly pay for molecular dynamics in the United States is $80,687.00, according to ZipRecruiter salary data. Most workers in this role earn between $69,000.00 and $98,500.00 per year, depending on experience, location, and employer.

What is molecular dynamics?

A Molecular Dynamics job typically involves using computational simulations to study the physical movements of atoms and molecules. Professionals in this field use specialized software and high-performance computing to analyze molecular interactions in fields like drug discovery, materials science, and biophysics. They may work in academia, pharmaceuticals, or research labs to model molecular behavior and predict system properties. Strong backgrounds in physics, chemistry, and programming are often required.

What does someone working in molecular dynamics do?

Professionals in Molecular Dynamics frequently work on computational research projects that involve simulating the behavior of molecules to gain insights into physical, chemical, or biological processes. Daily tasks often include designing simulation experiments, running large-scale computations, analyzing simulation results, and preparing reports or publications. Collaboration with multidisciplinary teams—such as chemists, biologists, and materials scientists—is common to ensure projects address real-world scientific questions. This role may also involve presenting findings at meetings or conferences and staying current with advancements in simulation techniques. Being part of a collaborative research environment offers continuous learning and the opportunity to contribute to innovative discoveries.

What are the key skills and qualifications needed to thrive in molecular dynamics?

To excel in a Molecular Dynamics role, a strong background in physics, chemistry, computational modeling, and a relevant advanced degree (often a Ph.D.) are essential. Experience using molecular simulation software such as GROMACS, AMBER, or LAMMPS, as well as proficiency in programming languages like Python, C++, or Fortran, is typically required. Strong analytical thinking, meticulous attention to detail, and effective communication skills are valuable soft skills in this field. These qualifications are critical for accurately modeling molecular systems, interpreting complex data, and collaborating effectively with interdisciplinary research teams.

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Molecular Dynamics jobs near you
Infographic showing various Molecular Dynamics job openings in the United States as of August 2026, with employment types broken down into 100% Full Time. Highlights an 100% In-person job distribution, with an average salary of $80,687 per year, or $38.8 per hour.

Computational Chemistry Lead

Astellas Pharma, Inc.

Cambridge, MA • On-site

Full-time

Medical, Dental, Vision, Life, Retirement, PTO

Re-posted 2 days ago

Job description

Computational Chemistry
About Astellas
Astellas is a global life sciences company committed to turning innovative science into VALUE for patients. We provide transformative therapies in disease areas that include oncology, ophthalmology, urology, immunology and women's health. Through our research and development programs, we are pioneering new healthcare solutions for diseases with high unmet medical need. Learn more at Astellas.com.
Are you driven to make a real difference in the lives of patients?
We're seeking passionate individuals who thrive in dynamic environments, embrace new ideas, and aren't afraid to take intelligent risks. People who act with unwavering integrity and are deeply committed to making a tangible impact.
Purpose & Scope
This role supports drug discovery efforts by applying advanced computational chemistry techniques to design and optimize small-molecule therapeutics. The position requires close collaboration with internal teams and external CROs to accelerate candidate selection and improve research productivity. The Computational Chemist will contribute to strategic decisions and innovation across multiple therapeutic areas
Role and Responsibilities
  • Computational Drug Design: Apply molecular modeling, docking, molecular dynamics, homology modeling, and structure-based design to guide compound optimization
  • Use cheminformatics and machine learning tools to analyze SAR, ADME/Tox profiles, and predict compound behavior.
  • Develop generative models, reinforcement learning pipelines, and predictive analytics for compound design and optimization
  • Curate chemical libraries, manage data pipelines, and support SAR/ADME analysis
  • Serve as lead or co-lead in projects, setting project goals and defining plans
  • Drug Design & Synthesis: Design novel compounds based on ADME and SAR principles; optimize lead molecules for potency, selectivity, and pharmacokinetics.
  • Data Analysis & Reporting: Analyze large datasets from simulations and experimental data with scientific rigor; interpret computational results and prepare detailed research reports and present findings internally and externally to technical and non-technical audiences.
  • Cross-functional Collaboration: Work closely with medicinal chemistry, biology, pharmacology, protein science, and preclinical teams to ensure drug candidates meet efficacy and safety standards. Participate in program-related meetings and contribute strategic insight
  • Intellectual Property: Identify and protect IP through patent filings and strategic documentation. Ensure accurate documentation of compound synthesis and project data
  • Foster a collaborative, transparent, and creative team environment that drives innovation and invention. Close partnership with colleagues in Japan is expected.
  • Technology Integration: Explore and apply cutting-edge technologies and global scientific trends to enhance research capabilities
  • Stay current with scientific literature and emerging technologies
  • Manage team priorities and resources in alignment with the company's overall I-Lab strategy and objectives.

CRO Management
  • Oversee computational chemistry execution at CROs, including troubleshooting and performance enhancement
  • Evaluate and onboard new CROs to improve cost-efficiency and research quality
  • Maintain weekly communication and productivity tracking with CRO teams

Required Qualifications:
  • Ph.D. in Computational Chemistry, Cheminformatics, Medicinal Chemistry, or related field; or M.S. with 5+ years of industry experience
  • Proven experience in computational support of small molecule drug discovery.
  • Familiarity with AI-driven drug design
  • Proficiency in software packages such as Schrodinger, MOE, OpenEye, Rosetta, and scientific programming (Python, Pipeline Pilot).
  • Strong understanding of organic and synthetic chemistry concepts.
  • Experience managing CRO relationships and external collaboration
  • Deep understanding of advancements in drug discovery, emerging technologies, and industry trends, and experience applying this knowledge to enhance research strategies.

Technical Expertise:
  • Molecular Modeling & Simulation: Proficient in structure-based drug design (SBDD), including molecular docking, molecular dynamics (MD), and free energy perturbation (FEP).
  • Skilled in homology modeling, pharmacophore modeling, and quantum mechanics/molecular mechanics (QM/MM) methods.
  • Experienced in cryptic pocket identification and virtual screening for challenging targets

  • Chemoinformatics & Data Science: Applies cheminformatics tools to analyze structure-activity relationships (SAR), ADME/Tox profiles, and compound clustering.
  • Uses machine learning (ML) and AI-driven platforms for compound prioritization, generative design, and predictive modeling.
  • Familiar with scripting languages like Python and platforms such as Schrödinger, MOE, and KNIME

  • Drug Discovery Integration: Designs and optimizes small molecules for potency, selectivity, and pharmacokinetics.
  • Collaborates with medicinal chemists, biologists, and pharmacologists to guide compound progression from hit to lead

Skills:
  • Strong collaboration and teamwork abilities.
  • Excellent oral and written communication in English.
  • Strategic thinking and problem-solving capabilities
  • Strong communication and influencing skills
  • Highly collaborative win-win mindset is essential

Working Environment
  • This position is based in Cambridge, MA and will require on-site work.

What awaits you at Astellas?
  • Global collaboration: Become part of a connected global business of like-minded life science leaders, all dedicated to improving patients' lives worldwide. Real-world patient impact: Contribute to transformative therapies that reach patients around the world, knowing your work makes a difference every day.
  • Relentless Innovation: Join a company at the forefront of scientific breakthroughs, where you'll have the opportunity to shape the future of healthcare.
  • A Culture of Growth: Chart your own course within a supportive environment that values your contributions, champions your development, and empowers you to pursue your passions.

Our Organizational Values and Behaviors
Values: Innovation, Integrity and Impact sit at the heart of what we do.
Behaviors: We come together as 'One Astellas', working with courage and a sense of urgency. We are outcome focused and consistently take accountability for our personal contribution.
Salary Range
$119,000-$170,000 (Final compensation will be determined based on a variety of factors, including but not limited to skills, experience and organizational equity considerations)
Benefits:
  • Medical, Dental and Vision Insurance
  • Generous Paid Time Off options, including Vacation and Sick time, plus national holidays including year-end shut down
  • 401(k) match and annual company contribution
  • Company paid life insurance
  • Annual Corporate Bonus and Quarterly Sales Incentive for eligible positions
  • Long Term Incentive Plan for eligible positions
  • Company fleet vehicle for eligible positions
  • Referral bonus program

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