Associate Scientist, Post Doc Fellow – Computational Chemistry

Caraway Therapeutics, Inc.; Boston (MA); On-site; USD 79,000 - 125,000; Full time

Benefits offered by this job

Medical, dental, vision benefits

401(k) retirement plan

Paid holidays

Vacation and sick leave

Job summary

Caraway Therapeutics, Inc. in Boston, MA is seeking an Associate Scientist, Postdoctoral Fellow in Computational Chemistry to advance physics-based simulations and free energy perturbation studies.

You will design and execute MD-based binding calculations, analyze results, and contribute to method development within a collaborative Modeling & Informatics team. The role requires a PhD (or anticipated by Spring 2027) in chemistry/biochemistry/biophysics with computational emphasis, strong coding

Qualifications

• PhD required or expected by Spring 2027.
• PhD in chemistry, biochemistry, biophysics or equivalent with computational emphasis.
• Experience in molecular dynamics simulations and computing.

Responsibilities

• Design, execute, and analyze free energy calculations for protein-ligand systems.
• Develop analysis methods to extract binding information from FEP data.
• Interpret results with experimental data and structure–activity relationships.
• Present findings at internal meetings, external conferences, and in publications.

Skills

Molecular dynamics

Python

Data analysis workflows

Statistical mechanics

Thermodynamics

Independent work

Publications

Education

PhD in chemistry/biochemistry/biophysics (computational)

Tools

NAMD

AMBER

GROMACS

Job description

Job Description

Associate Scientist, Postdoctoral 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 a 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.

Responsibilities

• 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

Qualifications

• 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

Required Experience and Skills

• 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

Preferred Experience and Skills

• 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

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

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

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

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.

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

US and Puerto Rico Residents Only

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

EEOC Know Your Rights

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We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

Learn more about your rights, including under California, Colorado and other US State Acts

Primary location for this posting is

USA - Massachusetts - Boston (MA Parcel B Laboratory)

Where required by law, the compensation range for this role is provided below.

The salary range for the primary location of this role is:
$79,200.00 - $124,700.00

This range reflects the Company's reasonable expectation of the base salary applicable to this role at the time of posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs. 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. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits .

Additional location(s): Please note the salary range above applies to the Primary Location of the position. Where a role has other listed locations, different compensation guidelines may apply. You may find the salary ranges for additional locations below. If the salary range is not listed for the location you are applying to, our Talent Acquisition team will provide further information to you relevant to your location.

Additional location(s) Compensation Information

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

Los Angeles Residents Only: 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

Employee Status: Regular

Relocation: Domestic

VISA Sponsorship: Yes

Travel Requirements: 10%

Flexible Work Arrangements: Not Applicable

Shift: Not Indicated

Valid Driving License: No

Hazardous Material(s): N/A

Job Posting End Date

10/26/2026

*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.