Associate Principal Scientist, Molecular Modeling

Job Description We are a global biopharmaceutical leader with a diverse portfolio of prescription medicines, oncology, vaccines and animal health products. We are driven by our purpose to develop and deliver innovative products that save and improve lives. With 69,000 employees operating in more than 140 countries, we offer state of the art laboratories, plants and offices that are designed to inspire our employees as we learn, develop and grow in our careers. We are proud of our over 125 years of service to humanity and continue to be one of the world’s biggest investors in Research & Development. We are seeking a motivated Associate Principal Scientist to join our Digital Insights team within the Development Sciences and Clinical Supply (DSCS) Digital Technologies organization. The DSCS Digital Technologies organization is responsible for the invention and application of new digital tools/workflows to support scientists across drug substance development, drug product development and analytical development. Digital is the multiplier that will allow DSCS to deliver better experiments faster, efficient filing and launch, more robust supply chains and higher-confidence decisions across the portfolio. We aspire to embed digital technologies into the fabric of DSCS culture to drive transformational impact, by innovating solutions through strong partnership in the domains of Data Science, Data Analysis, Informatics, Multi-Omics, Predictive Science, and Data Engineering. The tools that we develop are as diverse as the teams developing them, and in this Associate Principal Scientist role, the successful candidate will leverage their expertise in atomistic modeling of drug substance and drug formulations with an ability to apply predictive sciences to support our Company’s pipeline of antibodies, small molecules, peptides, biologics, conjugates, and vaccines. This role will allow the candidate to solve complex scientific challenges through application of data modeling, analysis, and visualization tools. Initial focus will be related to modeling of antibodies and small molecule drug formulations. The successful candidate is expected to collaboratively work with process, formulation, computational, and analytical scientists, understand their problem statements, and collaboratively implement and apply predictive science solutions. The candidate must be able to work proactively and independently and influence decisions and solutions spanning a wide diversity of problem statements across our Research & Development Division. The role will require the candidate to network across a range of departments and effectively collaborate with stakeholders. The candidate should exemplify positive ways of working which support diversity, inclusion, and a positive culture. Primary Responsibilities Expert execution of atomistic molecular modeling and molecular dynamics simulations. Application of predictive approaches to address scientific problems across pharmaceutical characterization techniques. Application of data science workflows to address pipeline challenges across all modalities with initial emphasis on biologics. Application and generation of data analysis, and visualization workflows. Input on development of dashboards, reports, and data exports. Influence definition of digital strategy. Lead and manage projects, including scope definition, stakeholder alignment, milestone tracking, and delivery against project timelines Build strong partnerships with business stakeholders to gather requirements for new digital and data solutions which will have direct pipeline impact. Demonstrate excellent interpersonal, communication, and collaboration skills Demonstrate a clear ability to perform impactful scientific innovation in a team-oriented manner that builds trusted partnerships across vast stakeholder networks Have a demonstrated ability to publish and present research, including an established track record of interaction with the broader academic community Education Minimum Requirements A Ph.D. in Computational Chemistry, Chemistry, Biochemistry, Engineering, Data Science, Mathematics, Physics, Biology, Pharmaceutical Sciences, or a closely-related field with at least 4 years of relevant experience. A M.S. in Computational Chemistry, Chemistry, Biochemistry, Engineering, Data Science, Mathematics, Physics, Biology, Pharmaceutical Sciences, or a closely-related field with at least 6 years of relevant experience. A B.S. in Computational Chemistry, Chemistry, Biochemistry, Engineering, Data Science, Mathematics, Physics, Biology, Pharmaceutical Sciences, or a closely-related field with at least 8 years of relevant experience. Required Experience and Skills Expertise in atomistic modeling (direct experience with antibodies and at least one other modality: small molecules, peptides, biologics, conjugates, and vaccines). Expertise in executing molecular dynamics simulations of multi-component systems. Expertise across multiple computational modeling platforms such as: Rosetta, Gromacs, Amber, Schrodinger, MOE, Gaussian, AlphaFold, etc. Familiar with programming in R and/or Python and Posit/RStudio/Jupyter Experience with one or more data visualization tools (Shiny, Spotfire, Dash, PowerBI, Streamlit, or Tableau). Excellent verbal and written communications skills. Work independently and be able to collaborate as a team. Preferred Experience and Skills Multi-scale modeling including coarse grained molecular dynamics. Familiarity with Machine learning/Gen AI. Experience with pharmaceutical drug product development involving formulation design. Knowledge of development of chemical matter across one or more modalities. Track record of impact in the pharmaceutical industry with relevant examples directed towards pipeline objectives. Development of dashboards, reports, and data exports. Required Skills: Adaptability, Biopharmaceutical Industry, Biopharmaceuticals, Chromatographic Techniques, Computational Chemistry, Data Analysis, Data Science, High Resolution Mass Spectrometry (HRMS), Liquid Chromatography-Mass Spectrometry (LC-MS), Mass Spectrometry Analysis, Molecular Modeling, Pharmaceutical Development, Pharmaceutical Sciences Preferred Skills: Current Employees apply HERE Current Contingent Workers apply HERE 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. Please click here if you need an accommodation during the application or hiring process. 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 EEOC GINA Supplement 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 The salary range for this role is $142,400.00 - $224,100.00 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. More information about benefits is available at You can apply for this role through (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting. 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 Search Firm Representatives Please Read Carefully 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 deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. Employee Status: Regular Relocation: Domestic VISA Sponsorship: No Travel Requirements: 10% Flexible Work Arrangements: Hybrid Shift: Not Indicated Valid Driving License: No Hazardous Material(s): n/a Job Posting End Date: 07/9/2026 *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. Our company is a global health care leader with a diversified portfolio of prescription medicines, vaccines and animal health products. The difference between potential and achievement lies in the spark that fuels innovation and inventiveness; this is the space where we have codified our legacy for over a century. Our success is backed by ethical integrity, forward momentum, and an inspiring mission to achieve new milestones in global healthcare.