Senior Scientist, Cheminformatics

Job Description

Position Overview:

Our Company is currently seeking an exceptional, highly motivated Senior Scientist, Cheminformatics to join the Modeling & Informatics group within Discovery Chemistry. The successful candidate will join multidisciplinary discovery teams to drive the development and application of advanced cheminformatics workflows, machine learning models, and data-driven methods. This role focuses on accelerating drug discovery pipelines across both small molecules and emerging modalities—such as cyclic peptides, macrocycles, and DNA-Encoded Library platforms—in close partnership with computational and medicinal chemists.

Key Responsibilities

• · Computational Chemistry Partnership: Partner closely with computational and medicinal chemists on Discovery Chemistry project teams to address challenging structure-activity relationships and multi-parameter optimization

• · Emerging Modalities & DNA-Encoded Library Informatics: Develop and deploy specialized informatics workflows for non-traditional modalities (cyclic peptides, macrocycles) and DNA-Encoded Library platforms, including combinatorial enumeration, selection data triage, and hit prioritization.

• · Workflow & Algorithm Development: Design, validate, and implement scalable cheminformatics and machine learning pipelines for predictive property modeling, virtual screening, and chemical library triage.

• · Data Infrastructure & Tooling: Establish robust, automated computational tools and data pipelines that bridge internal chemical data platforms and modern modeling frameworks.

• · Scientific Presence & Mentorship: Maintain an active external scientific presence through publications, conference presentations, and community engagement, while mentoring junior staff, interns, and co-ops.

Position Qualifications:

Required Education:

• · Ph.D. (or close to completion) in Cheminformatics, Computational Chemistry, Chemistry, Computer Science, Bioinformatics, or a related quantitative discipline; OR

• · M.S. degree with 4+ years of relevant industry/research experience.

Required Experience & Skills:

• · Demonstrated expertise in cheminformatics fundamentals (molecular representations, fingerprints, similarity search, tautomer enumeration, and conformer generation).

• · Strong programming proficiency in Python and scientific computing libraries (NumPy, SciPy, Pandas, scikit-learn).

• · Extensive hands-on experience with modern cheminformatics toolkits (e.g., RDKit, OpenEye Toolkits, or CDK).

• · Experience developing and validating machine learning or statistical QSAR models applied to chemical or biological data.

• · Demonstrated track record of effective collaboration in multidisciplinary scientific teams.

• · Strong oral and written communication skills, evidenced by peer-reviewed publications or presentations.

Preferred Experience:

• · Experience with computational design of cyclic peptides, macrocycles, or non-canonical peptide representations (e.g., HELM notation).

• · Experience with DNA-Encoded Library analysis, combinatorial enumeration, or NGS selection data deconvolution.

• · Familiarity with molecular modeling and structure-based design tools (e.g., Schrödinger, MOE) to facilitate cross-talk with molecular modelers.

• · Experience deploying containerized workflows (Docker), version control (Git), and utilizing Linux/high-performance computing (HPC) environments.

Required Skills

• Chemical Databases, Chemical Informatics, Cheminformatics, High Performance Computing (HPC), Machine Learning (ML), Molecular Design, Peptides, Structure Activity Relationship

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 primary location for this posting is:

• USA - New Jersey - Rahway
• 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 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:

• No Travel Required

Flexible Work Arrangements:

• Not Applicable

Shift:

• Not Indicated

Valid Driving License:

• No

Hazardous Material(s):

• NA

Job Posting End Date:

• 11/30/2026*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.