Senior Scientist Computational Chemistry

MSD; West Point (PA); On-site; USD 129,000 - 203,000; Full time

Benefits offered by this job

Medical, dental, vision insurance

401(k) retirement plan

Paid holidays and vacation

Job summary

Merck & Co., Inc. in West Point, PA seeks a creative computational chemist and data scientist to join the Modeling and Informatics group. You will balance direct discovery support with data science, applying structure‑based design, docking, and ML to accelerate therapeutic discovery.

You will collaborate with global teams, develop AI/ML workflows, and mentor peers while advancing computational methods in drug design. This is an on‑site role with a strong pipeline focus.

Qualifications

• PhD in Computational Chemistry, Chemoinformatics, Chemistry, Data Science, or equivalent with a computational emphasis.
• Proficiency in molecular modeling (docking, MD, QM) and Linux; strong Python skills (RDKit, OpenEye, Pandas, NumPy, SciPy).
• Hands-on ML experience (e.g., scikit-learn, PyTorch, TensorFlow) applied to chemical/biological data; strong collaboration skills.

Responsibilities

• Serve as primary computational chemistry partner on discovery teams for design and optimization of candidates.
• Design, benchmark, and deploy predictive AI/ML models for molecular properties and endpoints; build reusable Python toolkits.
• Mentor peers and share reusable workflows; contribute to department culture and scientific coding practices.

Skills

Chemistry

Computational Chemistry

Data Science

Python

PyTorch

Machine Learning

QSAR

HPC

Molecular Dynamics

Molecular Modeling

DL/ML for drug design

Education

PhD in Computational Chemistry/Chemoinformatics/Chemistry/Data Science

Tools

RDKit

OpenEye toolkits

Pandas

NumPy

SciPy

scikit-learn

PyTorch

TensorFlow

Job description

Position 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. 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. The successful candidate will join multidisciplinary, highly collaborative discovery teams both locally and across the global network to invent novel medicines. This role is uniquely designed as a hybrid position, balancing direct early discovery project support (~50%) and design, and deployment of data science and machine learning models (~50%). They will apply advanced computational techniques to active drug discovery programs and develop innovative computational methods, algorithms, and predictive tools to solve foundational problems in drug design.

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, Chemoinformatics, 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 modelling, 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 modelling, 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 modelling software packages (e.g., Schrödinger, MOE, Openeye); experience with modern software development practices (Git/GitHub, containerisation with Docker, cloud computing environments such as AWS or Google cloud); experience developing and deploying interactive data visualisation 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

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)

Preferred 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)

Eligibility

US and Puerto Rico Residents Only:

Equal Opportunity and Inclusion

We are 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, colour, 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.

Salary and Benefits

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 Information

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.

Job Posting End Date

11/6/2026

About the Company

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 Material(s): NA.

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.