Associate Scientist, Post Doc Fellow - Computational Chemistry

We are seeking a highly motivated postdoctoral researcher with expertise in physics-based simulation and free energy perturbation (FEP) calculations to join our Modeling & Informatics (M&I) department in Boston, MA, USA. Our M&I team is an inclusive group of approximately 50 computational chemists, cheminformaticians, data scientists, and machine learning specialists who employ state-of-the-art capabilities to drive drug design. Join us to research innovative free energy methods to aid the discovery of better molecules.

• Design, execute, and analyze free energy calculations of protein-ligand binding and biomolecular systems
• Investigate analysis methods for maximal information extraction from free energy calculations, including the atomic drivers of affinity
• Interpret simulation results in the context of experimental data and structure-activity relationships
• Participate in methods development, investigate and implement novel computational methods, and contribute to internal workflows for M&I
• Present scientific findings via internal meetings, external conferences, and scientific publications

• Must currently hold a PhD OR
• Receive a Ph.D. no later than spring 2027
• Ph.D. in chemistry, biochemistry, biophysics, or equivalent with a computational emphasis

• Strong expertise in molecular dynamics or related atomistic simulation methods, including experience with one or more simulation packages such as NAMD, AMBER, GROMACS
• Proficiency in programming/scripting, preferably Python, and familiarity with data analysis workflows
• Solid understanding of statistical mechanics, thermodynamics, and molecular interactions
• Demonstrated ability to work independently and collaboratively in a research environment
• Strong oral and written communication skills, with a proven publication record in computational chemistry or related journals

• Experience with enhanced sampling methods, free energy calculations, or alchemical approaches
• Familiarity with protein-ligand binding, protein dynamics, membrane systems, or nucleic acid simulations
• Exposure to high-performance computing environments and parallel computing
• Experience with automated simulation pipelines or workflow orchestration

As a postdoctoral fellow at our research laboratories, you will be exposed to a fast-paced, interdisciplinary drug discovery environment with opportunities to learn about the pharmaceutical industry and the impact of computational chemistry. You will have access to High Performance Computing and modern computational chemistry software packages. We are looking for a self-driven individual with a desire to research cutting-edge simulation methods to impact drug discovery.

The salary range for this role is: $82,000-$92,000

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits. Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days.

Chemistry, Computational Chemistry, Computational Methods, Data Science, Drug Design, Drug Discovery Research, Molecular Biophysics, Molecular Dynamics (MD), Molecular Modeling, Statistical Mechanics

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. If you need an accommodation during the application or hiring process.

We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring Ordinance

Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be…