Senior Scientist Computational Chemistry

Merck & Co.; West Point (PA); On-site; USD 129,000 - 203,000; Full time

Benefits offered by this job

Health insurance

401(k) plan

Paid holidays

Job summary

Merck & Co., Inc. in West Point, PA seeks a creative, self-motivated computational chemist and data scientist to join the Modeling and Informatics group.

You will drive candidate design, leverage AI/ML, and scale predictive workflows for medicinal chemistry and drug discovery. The role requires a PhD and hands-on experience in molecular modeling, ML, and Python, collaborating across global teams to advance therapeutics.

Qualifications

• PhD in Computational Chemistry, Chemoinformatics, Chemistry, Data Science, or equivalent with computational emphasis.
• Strong experience in molecular modeling, docking, QM, and ML applied to chemical data.
• Proven ability to communicate complex ML concepts to non-specialists.

Responsibilities

• Serve as the primary computational chemistry partner on multidisciplinary discovery teams to drive candidate design and optimization.
• Design molecules using structure- and ligand-based design, docking, and molecular dynamics.
• Develop and deploy predictive AI/ML models for molecular properties and ADMET endpoints.
• Build automated Python toolkits and workflows for cheminformatics and modeling.

Skills

Computational chemistry

Machine learning

Python programming

Team collaboration

Communication skills

Education

PhD in Computational Chemistry

Tools

Schrödinger

MOE

OpenEye

Git/GitHub

Docker

Job description

Job Description

Our company is seeking a creative, self-motivated computational chemist and data scientist with exceptional interpersonal and problem-solving skills to join the Modeling and Informatics group at our West Point, PA site. We are expanding our capability in computational medicinal chemistry, predictive data science, and machine learning to support our future organizational strategy for therapeutic discovery.

Position Description

Modeling and Informatics is a sub-team of Discovery Chemistry, who employ state-of-the-art capabilities in predictive sciences, AI/ML, and structure-based drug design to accelerate our invention of therapeutics for patients. We are an integral arm of both Discovery and Process Chemistry, and we collaborate seamlessly with teams across the globe to invent better molecules faster. With an unbiased approach to drug modalities, in-house access to the newest screening techniques, and world-class medicinal chemistry, we have a wealth of opportunities to impact our pipeline and ultimately save and improve patient lives.

Key Responsibilities

Discovery Project Support

• Serve as the primary computational chemistry partner on multidisciplinary discovery teams to drive candidate design and optimization through:
• Design of molecules utilizing existing computational drug discovery tools and techniques (structure- and ligand-based design, molecular docking, conformational sampling, molecular dynamics, and quantum mechanics).
• Informative data analysis, multi-parameter optimization (MPO), and molecular visualization.
• Protein construct design and binding-site ligandability assessment.
• Ligand library design, virtual screening (HTVS), and targeted library enumeration.
• Translating complex computational hypotheses and non-obvious model predictions into actionable synthetic targets for medicinal chemistry teams.
• Influencing teams in chemistry and adjacent functionalities by effectively communicating non-obvious insights from computational approaches to drive project decisions and inflections.

Data Science & Machine Learning Modeling/Development

• Partner with existing Data Science team to design, build, benchmark, and deploy predictive AI/ML models (e.g., QSAR, deep learning, graph neural networks) for molecular property prediction, ADMET endpoints, and potency predictions.
• Develop and deploy automated computational workflows and reusable Python toolkits/pipelines for cheminformatics and structural modeling.
• Explore and implement cutting-edge machine learning methodologies, including generative chemistry models, active learning, and foundation models for molecular design.
• Collaborate closely with Cheminformatics, Data Science, and IT teams to scale computational chemistry tools and integrate models into enterprise software platforms.
• Establish best practices for scientific code versioning, reproducible data analysis, and model validation.

Departmental Leadership & Culture

• Contributing to the overall wellbeing of our department by sharing knowledge, reusable workflows, and being invested in the success of your peers.
• Mentoring colleagues in emerging data science techniques and modern computational workflows.

Position Qualifications

Education Minimum Requirement

• PhD in Computational Chemistry, Chemoinformatic, Chemistry, Data Science, or equivalent, with a computational/data science emphasis.

Required Experience and Skills

• Proficiency in general molecular modeling techniques (docking, molecular simulation, homology modeling, quantum mechanics, ligand- and structure-based design) and Linux environment.
• Proficiency in scientific Python programming (e.g., RDKit, OpenEye toolkits, Pandas, NumPy, SciPy).
• Demonstrated hands‑on experience in applied machine learning, statistical modeling, or deep learning (e.g., scikit‑learn, PyTorch, TensorFlow) applied to chemical, biological, or physical datasets.
• Ability to communicate, collaborate, and deliver results as a member of multidisciplinary teams.
• A strong desire to learn and to innovate.
• Ability to manage multiple priorities simultaneously across project delivery and method development.
• Strong oral and written communication skills with the ability to convey complex ML/computational concepts to non-specialists.
• Evidence of creative application of computational approaches to problems of pharmaceutical interest.
• Track record of recent publications and/or presentations and external presence.

Preferred Experience and Skills

• Demonstrated impact on molecule design in a biopharmaceutical or biotechnology industry environment.
• Expertise with commercial modeling software packages (e.g., Schrödinger, MOE, Openeye).
• Experience with modern software development practices (Git/GitHub, containerization with Docker, cloud computing environments such as AWS or Google cloud).
• Experience developing and deploying interactive data visualization applications or web tools (e.g. Spotfire).
• Familiarity with generative AI for de novo molecule generation, geometric deep learning, or large language models for scientific data.
• Experience with automated workflow orchestration tools (e.g., KNIME or Pipeline Pilot).

Work Environment

NB: Because we believe our best work involves in-person collaborations, this is an on-site position located at our West Point, PA facility; it will not be remote work.

Required Skills

Chemical Informatics, Chemistry, Computational Chemistry, Computational Sciences, Data Science, Deep Learning, Drug Design, Drug Discovery Research, High Performance Computing (HPC), Machine Learning (ML), Molecular Dynamics (MD), Molecular Modeling, Python (Programming Language), PyTorch, Quantitative Structure Activity Relationship (QSAR)

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.

Equal Employment Opportunity Employer

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

Company Values

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 Rights

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

Primary Location for This Posting

USA - Pennsylvania - West Point

Salary Information

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

The salary range for the primary location of this role is: $129,000.00 - $203,100.00

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

Search Firm Representatives

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

Not Applicable

Shift

Not Indicated

Valid Driving License

No

Hazardous Materials

NA

Job Posting End Date

11/6/2026

*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.

Requisition ID

R423336